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)

Betacoronavirus 3'UTR   (Rfam: RF03122)

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
((N)G)U
(.ARY.)
(().NA.)
Y(AR)N
90.9
100.0
100.0
81.8
(.ARY.)

% of positive sequence with ORB





Deep neural network:

5-fold cross-validation: 99.8 %
(± 0.087 %)
Decision tree:

5-fold cross-validation: 89.4 %
(± 5.13 %)
D-ORB structure
D-ORB structure decision tree:

5-fold cross-validation: 64.3 %
(± 9.25 %)
of NC_009019.1/29956-30270
NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
(((((((((((..)))))))))))((.((((((((((.(.(((((((((((((((((((((...)))))))))))).))))))))))))))))).(((((((((((((((((((((((((((.(((..))))))))))))))).((((((((((((((((((((((((((((((((((((((((((((.((((((((((.((((((((...).)))))))))).))))))((((((..).)))))))))))))))))))))))))))))))))))))))))))....))))))).))))))))))))))))))))
...................................................................................................1...................................................................................................2...................................................................................................3...............
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.....
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abstract shape: ()(()(()(()())))

Number of sequences
Structure ORBs (out of 11) (%)
1 ((N)G)U
 10 90.9
>NC_004718.3/29421-29727
UAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
........................................................................((..........).)............................................................................................................................................................................................................................
>NC_009020.1/30152-30466
AGAGGCAUAAAUUGCCAAUUGAACGUAACAAGAGUCGAGGCGAUCGCUAGUGUUCUGGAAACCCCAUUACAUGAUGCAAUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUUUACUUACAGUGCAAGAAGGUAAGUGAACCCAUUUAAUUGAUAGCUGUCAUUUUAGUAAAGUGUGUAGCUAUAGAGAGAAGUUUAAAGACUGUCACCUCUGCGAGAUUGCAAGUGAACAGUGCCCCCUGGGAAGAGCUCUAUAGUGUGAAAUGUAAAUAAAAACAGCUAUUAUUCAAUUAGAUUAGGCUUUUUAGAUGAUUUGC
.............................................................................................................................................................................................((..........).)...............................................................................................................
>NC_003045.1/30698-31026
AAGAUGGAUGAGCCCUUUACUGAAGACACCUCAGAAAUAUAAGAGAAUGAACCUUAUGUCGGCACCUGGUGGUAACCCCUCGCAGGAAAGUCGGGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUGGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGGAAGAGCCAGCAUGUUAAGUUACCAUCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUC
.................................................................................................................................................................................((..............................................................................................................).).....................................
>NC_026011.1/30919-31234
AUACCCAGGGAAGCUCAGAAAUAUAAGAGAAUGAACCCUAUGUCGGCACUAGGUGGAUAAAACCUCGCUAGCCAGUCGGGAUAGGGCACUCUCUAUCAGAAUGGAUGUCUUGUCACUACAAUAGAUAGAGAAGGUUGUAGUGGACUAUAGAUUGCUUAGUUGAAAAUUAUUGUUGAUCAUGUAUAGUGUUGGAGCAGGUGAAAGAUGUGCGUACAUAAGUGACGACACGUGCCCAUGUGGAAGAGCCAGCAUGUUAAGUGAUCAGUAAUAGAUUAGUAAAUGGAUGAAGGUAAUCAUGGCCAAUUGGAAGAAUAAC
..................................................................................................................................................................((..............................................................................................................).).......................................
>NC_025217.1/31161-31481
CUCUGAAAUCUGAAAAAUUCGCAAGUAGUAAGGCGUAGUAUACCCUACCAGUAGGACUGGGUUGCUAUUCCUACACUUGUGCUGAAUGGAUUCUAUGUAUAGUGUAGCACAAGAAGACACUAUACACGUUUACUAUCACUGUCUUUGACAUUUAGUGUAUAGUUGAUUGGAGUAAUUACAAAGAAUACACACCGAGGCCACGCCGAGUAGGAACGAGGGUACAGUGUGAAAAGCCGAUGUCAAUGACCGGAAGAGCCAAUCAAUGUAAAAUUAAUAAUCAAAGAACCCCCAGUGAUUUUAAUAGCUUUUUAGUAGAAUUGC
.............................................................................................((...............................).)................................................................................................................................................................................................
>NC_039207.1/29818-30136
GAACCUUAAAAAGGUACAGUAAAAGUAACAAGAGUGAGGCAAUCGCUAGUGAAUGGAAACCCCAUGUCAUGAGGCAAUUGUCUACUCUUGCACAGAAUGGAAUCAUGUUGUAACUACAGUGCAAGAAGGUAGGUACAAUCCAUUUAAUUGAUAGCUAUGUUUUAGUAAAGUGUGUAGCUAUAGAGAGUAAGUUAAAGGUUAACACCGCUGCAUAAUUGGCCCUUGCAUGUGAUUAACGCCCCCUGGGAAGAGCUCUAUAGUGUGUAAUGUAAAUAAGAAUAGCUAUAAUUCAAUUAAUUCGGCUUAUUAGAUGAUUUGC
...................................................((...........).)............................................................................................................................................................................................................................................................
>NC_038294.1/29781-30099
UUGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGUAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
.......................................................................................................................................................................................................((.........................).)..........................................................................................
>NC_019843.3/29789-30107
UGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGCAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCUUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
.......................................................................................................................................................................................................((........................).)...........................................................................................
>NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...................................................................................................................................................................................................((.........................).)..........................................................................................
>NC_006213.1/30411-30713
ACCUCAGAAAUAUAAGAGAAUGAACCUUAUGUCGGCAUCUGGUGGUAACCCCUCGCAGAAAAGUCGAGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUUGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGAAGAGCCAGCAUGUUAAGUUACCACCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUCAC
........................................................................................................................................................................................((.............................).).....................................................................................
2 ((N)G)U
(.ARY.)
 9 81.8
>NC_039207.1/29818-30136
GAACCUUAAAAAGGUACAGUAAAAGUAACAAGAGUGAGGCAAUCGCUAGUGAAUGGAAACCCCAUGUCAUGAGGCAAUUGUCUACUCUUGCACAGAAUGGAAUCAUGUUGUAACUACAGUGCAAGAAGGUAGGUACAAUCCAUUUAAUUGAUAGCUAUGUUUUAGUAAAGUGUGUAGCUAUAGAGAGUAAGUUAAAGGUUAACACCGCUGCAUAAUUGGCCCUUGCAUGUGAUUAACGCCCCCUGGGAAGAGCUCUAUAGUGUGUAAUGUAAAUAAGAAUAGCUAUAAUUCAAUUAAUUCGGCUUAUUAGAUGAUUUGC
........................................................(...)..................................................................................................................((...................................................................................).)........................................................
>NC_003045.1/30698-31026
AAGAUGGAUGAGCCCUUUACUGAAGACACCUCAGAAAUAUAAGAGAAUGAACCUUAUGUCGGCACCUGGUGGUAACCCCUCGCAGGAAAGUCGGGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUGGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGGAAGAGCCAGCAUGUUAAGUUACCAUCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUC
........................................................................(...)....................................................................................................((..............................................................................................................).).....................................
>NC_025217.1/31161-31481
CUCUGAAAUCUGAAAAAUUCGCAAGUAGUAAGGCGUAGUAUACCCUACCAGUAGGACUGGGUUGCUAUUCCUACACUUGUGCUGAAUGGAUUCUAUGUAUAGUGUAGCACAAGAAGACACUAUACACGUUUACUAUCACUGUCUUUGACAUUUAGUGUAUAGUUGAUUGGAGUAAUUACAAAGAAUACACACCGAGGCCACGCCGAGUAGGAACGAGGGUACAGUGUGAAAAGCCGAUGUCAAUGACCGGAAGAGCCAAUCAAUGUAAAAUUAAUAAUCAAAGAACCCCCAGUGAUUUUAAUAGCUUUUUAGUAGAAUUGC
....(....)...................................................................................((...............................).)................................................................................................................................................................................................
>NC_004718.3/29421-29727
UAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
................(...)...........................................................................................((.....................................................................................................................................................).).........................................
>NC_006213.1/30411-30713
ACCUCAGAAAUAUAAGAGAAUGAACCUUAUGUCGGCAUCUGGUGGUAACCCCUCGCAGAAAAGUCGAGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUUGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGAAGAGCCAGCAUGUUAAGUUACCACCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUCAC
............................................(.....).....................................................................................................................................((.............................).).....................................................................................
>NC_009020.1/30152-30466
AGAGGCAUAAAUUGCCAAUUGAACGUAACAAGAGUCGAGGCGAUCGCUAGUGUUCUGGAAACCCCAUUACAUGAUGCAAUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUUUACUUACAGUGCAAGAAGGUAAGUGAACCCAUUUAAUUGAUAGCUGUCAUUUUAGUAAAGUGUGUAGCUAUAGAGAGAAGUUUAAAGACUGUCACCUCUGCGAGAUUGCAAGUGAACAGUGCCCCCUGGGAAGAGCUCUAUAGUGUGAAAUGUAAAUAAAAACAGCUAUUAUUCAAUUAGAUUAGGCUUUUUAGAUGAUUUGC
.........................................................(.....).............................................................................................................................((..........).)...............................................................................................................
>NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...........................................................(.....).................................................................................................................................((.........................).)..........................................................................................
>NC_038294.1/29781-30099
UUGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGUAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
..............................................................(.....)..................................................................................................................................((.........................).)..........................................................................................
>NC_019843.3/29789-30107
UGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGCAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCUUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
.............................................................(......)..................................................................................................................................((........................).)...........................................................................................
3 ((N)G)U
(.ARY.)
(().NA.)
 7 63.6
>NC_006213.1/30411-30713
ACCUCAGAAAUAUAAGAGAAUGAACCUUAUGUCGGCAUCUGGUGGUAACCCCUCGCAGAAAAGUCGAGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUUGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGAAGAGCCAGCAUGUUAAGUUACCACCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUCAC
.............................................(...)...........................................................((.......................................((.............................................................................................................).)............)..).......................
>NC_004718.3/29421-29727
UAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
................(...)....................................................................................((.....((.....................................................................................................................................................).).....)....)..............................
>NC_019843.3/29789-30107
UGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGCAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCUUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
.............................................................(....)........................................................................................((...................................................................((......).)................................................)....)..............................
>NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...........................................................(.....)........................................................................................((.......................................((.........................).).....................................................)....)...............................
>NC_009020.1/30152-30466
AGAGGCAUAAAUUGCCAAUUGAACGUAACAAGAGUCGAGGCGAUCGCUAGUGUUCUGGAAACCCCAUUACAUGAUGCAAUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUUUACUUACAGUGCAAGAAGGUAAGUGAACCCAUUUAAUUGAUAGCUGUCAUUUUAGUAAAGUGUGUAGCUAUAGAGAGAAGUUUAAAGACUGUCACCUCUGCGAGAUUGCAAGUGAACAGUGCCCCCUGGGAAGAGCUCUAUAGUGUGAAAUGUAAAUAAAAACAGCUAUUAUUCAAUUAGAUUAGGCUUUUUAGAUGAUUUGC
.........................................................(.....)........................................................................................((...................................((..........).)..........................................................................)....)...............................
>NC_038294.1/29781-30099
UUGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGUAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
..............................................................(....)........................................................................................((..........................................((........................).)......................................................)....)..............................
>NC_039207.1/29818-30136
GAACCUUAAAAAGGUACAGUAAAAGUAACAAGAGUGAGGCAAUCGCUAGUGAAUGGAAACCCCAUGUCAUGAGGCAAUUGUCUACUCUUGCACAGAAUGGAAUCAUGUUGUAACUACAGUGCAAGAAGGUAGGUACAAUCCAUUUAAUUGAUAGCUAUGUUUUAGUAAAGUGUGUAGCUAUAGAGAGUAAGUUAAAGGUUAACACCGCUGCAUAAUUGGCCCUUGCAUGUGAUUAACGCCCCCUGGGAAGAGCUCUAUAGUGUGUAAUGUAAAUAAGAAUAGCUAUAAUUCAAUUAAUUCGGCUUAUUAGAUGAUUUGC
........................................................(...)......................................................................................((..........................((...................................................................................).)........................)....)..........................
4 ((N)G)U
(.ARY.)
(().NA.)
Y(AR)N
 6 54.5
>NC_038294.1/29781-30099
UUGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGUAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
..............................................................(....)...........................................................(..)..............(.(....................................................((........................).)...............................................................)..).......................
>NC_004718.3/29421-29727
UAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
................(...).........................................................(..).......................((.....((.....................................................................................................................................................).).....)....)..............................
>NC_019843.3/29789-30107
UGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGCAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCUUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
.............................................................(....)...........................................................(..)..............(.(.............................................................................((......).).........................................................)..).......................
>NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...........................................................(.....)...........................................................(..).........................((.......................................((.........................).).....................................................)....)...............................
>NC_039207.1/29818-30136
GAACCUUAAAAAGGUACAGUAAAAGUAACAAGAGUGAGGCAAUCGCUAGUGAAUGGAAACCCCAUGUCAUGAGGCAAUUGUCUACUCUUGCACAGAAUGGAAUCAUGUUGUAACUACAGUGCAAGAAGGUAGGUACAAUCCAUUUAAUUGAUAGCUAUGUUUUAGUAAAGUGUGUAGCUAUAGAGAGUAAGUUAAAGGUUAACACCGCUGCAUAAUUGGCCCUUGCAUGUGAUUAACGCCCCCUGGGAAGAGCUCUAUAGUGUGUAAUGUAAAUAAGAAUAGCUAUAAUUCAAUUAAUUCGGCUUAUUAGAUGAUUUGC
........................................................(...)............................................................(..)......................((..........................((...................................................................................).)........................)....)..........................
>NC_009020.1/30152-30466
AGAGGCAUAAAUUGCCAAUUGAACGUAACAAGAGUCGAGGCGAUCGCUAGUGUUCUGGAAACCCCAUUACAUGAUGCAAUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUUUACUUACAGUGCAAGAAGGUAAGUGAACCCAUUUAAUUGAUAGCUGUCAUUUUAGUAAAGUGUGUAGCUAUAGAGAGAAGUUUAAAGACUGUCACCUCUGCGAGAUUGCAAGUGAACAGUGCCCCCUGGGAAGAGCUCUAUAGUGUGAAAUGUAAAUAAAAACAGCUAUUAUUCAAUUAGAUUAGGCUUUUUAGAUGAUUUGC
..........................................................(...)............................................................(..)........................((....................................((..........).)...........................................................................)....)..............................

>NC_004718.3/29421-29727
UAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
........................................................................((..........).)............................................................................................................................................................................................................................
................(...)...........................................................................................((.....................................................................................................................................................).).........................................
................(...)....................................................................................((.....((.....................................................................................................................................................).).....)....)..............................
................(...).........................................................(..).......................((.....((.....................................................................................................................................................).).....)....)..............................
>NC_009020.1/30152-30466
AGAGGCAUAAAUUGCCAAUUGAACGUAACAAGAGUCGAGGCGAUCGCUAGUGUUCUGGAAACCCCAUUACAUGAUGCAAUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUUUACUUACAGUGCAAGAAGGUAAGUGAACCCAUUUAAUUGAUAGCUGUCAUUUUAGUAAAGUGUGUAGCUAUAGAGAGAAGUUUAAAGACUGUCACCUCUGCGAGAUUGCAAGUGAACAGUGCCCCCUGGGAAGAGCUCUAUAGUGUGAAAUGUAAAUAAAAACAGCUAUUAUUCAAUUAGAUUAGGCUUUUUAGAUGAUUUGC
.............................................................................................................................................................................................((..........).)...............................................................................................................
.........................................................(.....).............................................................................................................................((..........).)...............................................................................................................
.........................................................(.....)........................................................................................((...................................((..........).)..........................................................................)....)...............................
..........................................................(...)............................................................(..)........................((....................................((..........).)...........................................................................)....)..............................
>NC_039207.1/29818-30136
GAACCUUAAAAAGGUACAGUAAAAGUAACAAGAGUGAGGCAAUCGCUAGUGAAUGGAAACCCCAUGUCAUGAGGCAAUUGUCUACUCUUGCACAGAAUGGAAUCAUGUUGUAACUACAGUGCAAGAAGGUAGGUACAAUCCAUUUAAUUGAUAGCUAUGUUUUAGUAAAGUGUGUAGCUAUAGAGAGUAAGUUAAAGGUUAACACCGCUGCAUAAUUGGCCCUUGCAUGUGAUUAACGCCCCCUGGGAAGAGCUCUAUAGUGUGUAAUGUAAAUAAGAAUAGCUAUAAUUCAAUUAAUUCGGCUUAUUAGAUGAUUUGC
...................................................((...........).)............................................................................................................................................................................................................................................................
........................................................(...)..................................................................................................................((...................................................................................).)........................................................
........................................................(...)......................................................................................((..........................((...................................................................................).)........................)....)..........................
........................................................(...)............................................................(..)......................((..........................((...................................................................................).)........................)....)..........................
>NC_038294.1/29781-30099
UUGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGUAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
.......................................................................................................................................................................................................((.........................).)..........................................................................................
..............................................................(.....)..................................................................................................................................((.........................).)..........................................................................................
..............................................................(....)........................................................................................((..........................................((........................).)......................................................)....)..............................
..............................................................(....)...........................................................(..)..............(.(....................................................((........................).)...............................................................)..).......................
>NC_019843.3/29789-30107
UGAUGUUAACACUGAUUAGUGUCACUCAAAGUAACAAGAUCGCGGCAAUCGUUUGUGUUUGGCAACCCCAUCUCACCAUCGCUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUGUAAUUACAGUGCAAUAAGGUAAUUAUAACCCAUUUAAUUGAUAGCUAUGCUUUAUUAAAGUGUGUAGCUGUAGAGAGAAUGUUAAAGACUGUCACCUCUGCUUGAUUGCAAGUGAACAGUGCCCCCCGGGAAGAGCUCUACAGUGUGAAAUGUAAAUAAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUAAUUAGAUGAUUUGC
.......................................................................................................................................................................................................((........................).)...........................................................................................
.............................................................(......)..................................................................................................................................((........................).)...........................................................................................
.............................................................(....)........................................................................................((...................................................................((......).)................................................)....)..............................
.............................................................(....)...........................................................(..)..............(.(.............................................................................((......).).........................................................)..).......................
>NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...................................................................................................................................................................................................((.........................).)..........................................................................................
...........................................................(.....).................................................................................................................................((.........................).)..........................................................................................
...........................................................(.....)........................................................................................((.......................................((.........................).).....................................................)....)...............................
...........................................................(.....)...........................................................(..).........................((.......................................((.........................).).....................................................)....)...............................
>NC_006213.1/30411-30713
ACCUCAGAAAUAUAAGAGAAUGAACCUUAUGUCGGCAUCUGGUGGUAACCCCUCGCAGAAAAGUCGAGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUUGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGAAGAGCCAGCAUGUUAAGUUACCACCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUCAC
........................................................................................................................................................................................((.............................).).....................................................................................
............................................(.....).....................................................................................................................................((.............................).).....................................................................................
.............................................(...)...........................................................((.......................................((.............................................................................................................).)............)..).......................
>NC_003045.1/30698-31026
AAGAUGGAUGAGCCCUUUACUGAAGACACCUCAGAAAUAUAAGAGAAUGAACCUUAUGUCGGCACCUGGUGGUAACCCCUCGCAGGAAAGUCGGGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUGGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGGAAGAGCCAGCAUGUUAAGUUACCAUCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUC
.................................................................................................................................................................................((..............................................................................................................).).....................................
........................................................................(...)....................................................................................................((..............................................................................................................).).....................................
>NC_025217.1/31161-31481
CUCUGAAAUCUGAAAAAUUCGCAAGUAGUAAGGCGUAGUAUACCCUACCAGUAGGACUGGGUUGCUAUUCCUACACUUGUGCUGAAUGGAUUCUAUGUAUAGUGUAGCACAAGAAGACACUAUACACGUUUACUAUCACUGUCUUUGACAUUUAGUGUAUAGUUGAUUGGAGUAAUUACAAAGAAUACACACCGAGGCCACGCCGAGUAGGAACGAGGGUACAGUGUGAAAAGCCGAUGUCAAUGACCGGAAGAGCCAAUCAAUGUAAAAUUAAUAAUCAAAGAACCCCCAGUGAUUUUAAUAGCUUUUUAGUAGAAUUGC
.............................................................................................((...............................).)................................................................................................................................................................................................
....(....)...................................................................................((...............................).)................................................................................................................................................................................................
>NC_026011.1/30919-31234
AUACCCAGGGAAGCUCAGAAAUAUAAGAGAAUGAACCCUAUGUCGGCACUAGGUGGAUAAAACCUCGCUAGCCAGUCGGGAUAGGGCACUCUCUAUCAGAAUGGAUGUCUUGUCACUACAAUAGAUAGAGAAGGUUGUAGUGGACUAUAGAUUGCUUAGUUGAAAAUUAUUGUUGAUCAUGUAUAGUGUUGGAGCAGGUGAAAGAUGUGCGUACAUAAGUGACGACACGUGCCCAUGUGGAAGAGCCAGCAUGUUAAGUGAUCAGUAAUAGAUUAGUAAAUGGAUGAAGGUAAUCAUGGCCAAUUGGAAGAAUAAC
..................................................................................................................................................................((..............................................................................................................).).......................................

ORB p-value ORB frequency
(per structure per nucleotide) 		Means
ratio
1 ((N)G)U < 0.001 2.82
NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...................................................................................................1...................................................................................................2...................................................................................................3...............
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.....
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2 (.ARY.) < 0.001 1.46
NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...................................................................................................1...................................................................................................2...................................................................................................3...............
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.....
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3 (().NA.) < 0.001 1.84
NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...................................................................................................1...................................................................................................2...................................................................................................3...............
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.....
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4 Y(AR)N 0.00188 1.58
NC_009019.1/29956-30270
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
UUCAGAGGCUUGAAUGCCAAUGAAGAGUAACAAGAGUUGAGGCAACUGCUAGCGUUCAGGUAACCCCUUUACGUGAUGCAUUUGUCCACUCUUGCACAGAAUGGAAUCAUGUUAAACUUACAGUGCAAGAAAGUAAGUUAACCCAUUUAAUUGAUAGCUAUGCUUAGUGUAAUGUGUAACUAUAGAGAGUAAUUUAAAGACUGUCACCUCUGCGUGAUUGCAAGUGAACAGUGCCCCUGUGGAAGAGCUCUAUAGUGUAAAGUGUAAAUAAAAAUAGCUAUUAUUCAAUUAGAUUAGGCUUAAUAGAUGAUUAAC
...................................................................................................1...................................................................................................2...................................................................................................3...............
.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.........2.........3.........4.........5.........6.........7.........8.........9.........0.........1.....
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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 .N. (URB) < 0.001 0.368
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).