JAR3D on RF00061

RF00061 Hepatitis C virus internal ribosome entry site

Input Summary

      00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000011111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111112222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222333333333333333333333333333333333333333333333333333333333
00000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555
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...((((((....)))))).......................((((.((((.....((((...(((.((...((((((.......))))))....)).)))....))))))))))))................(.((..(((((((((((((..((((((....))))))(((..(((((..((.(((((((........))).....)))).))....)))))..))).(((....))))))).)))))))))))).((((.((..(((((......)))))..)).))))((((....))))((........))....................((((.......)))).....
>NC_038882.1/2-354
CCAGCCCCCUGAUGGGGGCGACACUCCACCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>NC_004102.1/2-354
CCAGCCCCCUGAUGGGGGCGACACUCCACCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>EU234065.2/1-249
--------------------------------------------------------------------------------------------------------UGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>KJ439777.1/2-354
CCAGCCCCCUGAUGGGGGCGACACUCCACCAUGGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>MN977327.1/1-292
-------------------------------------------------------------UUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCCAGGACGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCUGGAAAUUUGGGCGUGCCCCCGCAAGACCGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>AY587845.1/1-281
------------------------------------------------------------------------AGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGCCCGGCCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUC
>AJ851228.1/1-327
---------------------------ACCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUCAAACCCGCUCUAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>KY348757.1/1-317
------------------------------------CACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAAGACCGGGUCCUUUC--UUGGAUU-AACCCGCUCUAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>KJ439768.1/2-354
CCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGAUCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUC--UUGGAU-AACCCCGCUCAAUGCCUGGAGAUUUGGGCAUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACAAAUC
>KX767023.1/1-286
-------------------------------------------------------------------CAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>EU234061.2/1-302
---------------------------------------------------AACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>AB677533.1/2-354
CCCGCCCCCUGAUGGGGGCGACACUCCGCCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUACCGGAAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGUCCGGUCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUC
>MW689975.1/1-348
------CCCUGAUGGGGGCGACACUCCGCCACGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUUAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>MW689965.1/9-361
CCAGCCCCCGAUUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>MW689971.1/1-317
------------------------------------CACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACCGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>MW690013.1/1-337
-----------------GCGACACUCCGCCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUCUAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>KC248199.1/2-354
CCAGCCCCCUGAUGGGGGCGACACUCCACCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGAUCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACAAAUC
>NC_009823.1/2-353
CCCGCCCCU-AAUAGGGGCGACACUCCGCCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGCCCGGCCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACAAAUC
>AF169004.1/2-353
CCCGCCCCU-AAUAGGGGCGACACUCCGCCAUGAACCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGCCCGGCCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAAC
>JX227965.1/1-276
-----------------------------------------------------------------------------CUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUGUGCCUGGCCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAGAUC
>KC197233.1/1-326
---------------------------GCCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGCCCGGCCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUC
>AB047639.1/2-353
CCUGCCCCU-AAUAGGGGCGACACUCCGCCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGCCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGCCCGGCCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGCGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACAAAUC
>MK548369.1/1-334
-------------------GACACUCCGCCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUURCCGGAAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGUCCGGUCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCUAGUAGCGUUGGGUUGCGAACGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUC
>AY232740.1/1-317
------------------------------------CACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUACCGGAAAGACUGGGUCCUUUC--UUGGAC-AAACCCACUCUAUGUCCGGUCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUC
>KC197230.1/1-326
---------------------------GCCAUGAAUCACUCCCCUGUGAGGAACUUCUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAAGACUGGGUCCUUUC--UUGGAU-AAACCCACUCUAUGCCCGGCCAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUC
>NC_009824.1/2-352
CCUGCCUCU--UACGAGGCGACACUCCACCAUGGAUCACUCCCCUGUGAGGAACUUCUGUCUUCACGCGGAAAGCGCCUAGCCAUGGCGUUAGUACGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCUGGGGUGACCGGGUCCUUUC--UUGGAGC-AACCCGCUCAAUACCCAGAAAUUUGGGCGUGCCCCCGCGAGAUCACUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>KY620603.1/1-351
CCUGAUGCU--UAGGAGGCGACACUCCACCAUGGAUCACUCCCCUGUGAGGAACUUCUGUCUUCACGCGGAAAGCGCCUAGCCAUGGCGUUAGUACGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCUGGGGUGACCGGGUCCUUUC--UUGGAAC-AACCCGCUCAAUACCCAGAAAUUUGGGCGUGCCCCCGCGAGAUCACUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>KJ470619.1/2-353
CCUGCCUCU--UUCGAGGCGACACUSCACCAUGGAUCACUCCCCUGUGAGGAACUUCUGUCUUCACGCGGAAAGCGCCUAGCCAUGGCGUUAGUACGAGUGUCGUGCAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCUGGGGUGACCGGGUCCUUUC--UUGGAACAAACCCGCUCAAUACCCAGAAAUUUGGGCGUGCCCCCGCGAGAUCACUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>JF735124.1/2-352
CCUGCCUCU--UUCGAGGCGACACUCCACCAUGGAUCACUCCCCUGUGAGGAACUUCUGUCUUCACGCGGAAAGCGUCUAGCCAUGGCGUUAGUACGAGCGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCCCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCCAUGCCUGGGUAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUC
>MN628597.1/4-355
GGGUCCUGG-AGGCGAGGCGACACUCCACCAUGGAUCACUCCCCUGUGAGGAACUUCUGUCUUCACGCGGAAAGCGCCUAGCCAUGGCGUUAGUACGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCUGGGGUGACCGGGUCCUUUC--UUGGAAC-AACCCGCUCAAUACCCAGAAAUUUGGGCGUGCCCCCGCGAGAUCACUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUC
>KY620874.1/10-360
GGAUCCUCU--CUCGAGGCGACACUCCACCAUGAAUCACUCCCCUGUGAGGAACUUCUGUCUUCACGCGGAAAGCGUCUAGCCAUGGCGUUAGUACGAGUGUCGUGCAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCCGGGACGACCGGGUCCUUUC--UUGGAAC-AACCCGCUCAAUGCCCGGAAAUUUGGGCGUGCCCCCGCGAGAUCACUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>JF735122.1/2-352
CCUGCCUCU--UUCGAGGCGACACUCCACCAUGAACCACUCCCCUGUGAGGAACUUCUGUCUUCACGCGGAAAGCGUCUAGCCAUGGCGUUAGUACGAGUGUCGUGCAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCCGGGUUGACCGGGUCCUUUC--UUGGAAC-CACCCGCUCAAUGCCCGGAAAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>NC_009825.1/1-292
-------------------------------------------------------------UUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUUGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUUCGGAACCGGUGAGUACACCGGAAUCGCCGGGAUGACCGGGUCCUUUC--UUGGAUU-AACCCGCUCAAUGCCCGGAAAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGCGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>KM043284.1/2-353
CCUGCUCUC-UAUGAGAGCAACACUCCACCAUGAACCGCUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUUGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCCGGGAUGACCGGGUCCUUUC--UUGGAUU-AACCCGCUCAAUGCCCGGAAAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>FJ462437.1/2-353
CCUGCUCUC-UAUGAGAGCAACACUCCACCAUGAACCGCUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUUGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCCGGGAUGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCCGGAAAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>NC_009826.1/1-292
-------------------------------------------------------------UUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGAACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAUGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCCGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>MH427311.1/2-352
CCCGCCCCU-UAUUGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGAACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAUGACCGGGUCCUUUC--UUGGAU-AAACCCGCUCAAUGCCCGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACGAAUC
>DQ278891.1/4-353
CCAGCCCCU--AAUGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGAUCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUU-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCSAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCAAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACACUUC
>LC435023.1/1-295
----------------------------------------------------------GUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--GUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUC
>MK327987.1/1-339
-------------CGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGAUCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGAUCACUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACAAAUC
>KC844040.1/2-351
CCAGCCCC--UAAUGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUY--UUGGAU-AAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUACUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUAC
>MG717928.1/2-355
CCAGCCCCU-UAACGGGGCGACACUCCGCCAUU-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCCAUUGGAUCAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUC
>KJ678751.1/1-312
--------------------------------------------UGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCCAUUGGAUCAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUC
>MG717925.1/1-298
----------------------------------------------------------GUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCCAUUGGAUCAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUC
>NC_009827.1/2-355
CCAGCCCCU-UAACGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUAGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCCAUUGGAUCAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGCGUUGGGUUGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>AY878652.1/1-321
--------------------------------UAAUCACUCCCCCUUGAGGAACUAAUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGAUCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACAGGGUCCUUUC--UUGGAUC-AACCCUCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>KM504115.1/2-352
CCAGCCCC--UAAUGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACUCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUCAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGSMACAUGAGCACACUUC
>EU158186.1/1-320
--------------------------------A-UCAACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGAUCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUC--UUGGAUC-AACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAUCAU
>MK139017.1/2-351
CCAGCCCCU--AACGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUAAUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGAUCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACAGGGUCCUUUC--UUGGAUC-AACCCUCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUC
>NC_030791.1/2-352
CCAGCCCCU--UACGGGGCGACACUCCGCCAUGAAUCACUCCCCUGCGAGGAACCACUGUCCUCACGCAGAAAGCGUCUAGCCAUGACGUUAGUAUGAGUGUCGUACAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAAGACUGGGUCCUUUC--UUGGAUC-AACCCACUCUAUGCCCGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUC
>MH590700.1/3-352
CCAGCCCCU--UAUGGGGCGACACUCCACCAUG-AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUACAGCCUCCAGGCCCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCGGGAUGACCGGGUCCUUUC--GUGGAUA-AACCCGCUCAAUGCCCGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUC

Rfam family RF00061 maps to these 33 chains: 4UJC|1|AC, 4UJD|1|BC, 4UPY|1|C, 4UPZ|1|C, 5A2Q|1|3, 5FLX|1|z, 5OA3|1|3, 6IP6|1|zz, 6IP8|1|zz, 7SYG|1|z, 7SYH|1|z, 7SYI|1|z, 7SYJ|1|z, 7SYK|1|z, 7SYL|1|z, 7SYM|1|z, 7SYN|1|z, 7SYO|1|z, 7SYP|1|z, 7SYQ|1|z, 7SYR|1|z, 7SYS|1|z, 7SYT|1|z, 7SYU|1|z, 7SYV|1|z, 7SYW|1|z, 7SYX|1|z, 9KKF|1|zz, 9KN5|1|zz, 9KN6|1|zz, 9KRP|1|zz, 9KZU|1|zz, 9KZX|1|zz See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Rfam family RF00061 is part of clan CL00017, which includes Rfam families RF00061, RF00209 .
There are 34 chains in PDB that we map to these Rfam families: 4C4Q|1|N, 4UJC|1|AC, 4UJD|1|BC, 4UPY|1|C, 4UPZ|1|C, 5A2Q|1|3, 5FLX|1|z, 5OA3|1|3, 6IP6|1|zz, 6IP8|1|zz, 7SYG|1|z, 7SYH|1|z, 7SYI|1|z, 7SYJ|1|z, 7SYK|1|z, 7SYL|1|z, 7SYM|1|z, 7SYN|1|z, 7SYO|1|z, 7SYP|1|z, 7SYQ|1|z, 7SYR|1|z, 7SYS|1|z, 7SYT|1|z, 7SYU|1|z, 7SYV|1|z, 7SYW|1|z, 7SYX|1|z, 9KKF|1|zz, 9KN5|1|zz, 9KN6|1|zz, 9KRP|1|zz, 9KZU|1|zz, 9KZX|1|zz . See them at RNA 3D Hub by filtering on Rfam family, clan, or chain.

Jump to results for:

Loop 1HL Column numbers: 9-14
Loop 2IL Column numbers: 46-48, 113-114
Loop 3IL Column numbers: 51-57, 109-110
Loop 4IL Column numbers: 60-64, 101-106
Loop 5IL Column numbers: 66-68, 97-99
Loop 6IL Column numbers: 69-73, 91-96
Loop 7HL Column numbers: 78-86
Loop 8IL Column numbers: 134-136, 256-257
Loop 9IL Column numbers: 137-140, 254-255
Loop 10IL Column numbers: 148-149, 244-246
Loop 11J4 Column numbers: 152-155, 170-171, 229-231, 240-241
Loop 12HL Column numbers: 160-165
Loop 13IL Column numbers: 173-176, 224-227
Loop 14IL Column numbers: 180-183, 215-220
Loop 15IL Column numbers: 184-186, 212-214
Loop 16IL Column numbers: 189-190, 203-209
Loop 17HL Column numbers: 192-201
Loop 18HL Column numbers: 233-238
Loop 19IL Column numbers: 262-264, 287-289
Loop 20IL Column numbers: 265-268, 283-286
Loop 21HL Column numbers: 272-279
Loop 22HL Column numbers: 296-301
Loop 23HL Column numbers: 306-315
Loop 24HL Column numbers: 340-348

Loop 1 Hairpin loop

Column numbers: 9-14 - This loop does not map to nucleotides in a 3D structure with xyz coordinates.

    Scored sequences and counts

    
    CUGAUG    7

    
    U-AAUA    3

    
    U--UUC    3

    
    C-UAUG    2

    
    U-UAAC    2

    
    --UAAU    2

    
    U--UAC    2

    
    CGAUUG    1

    
    G-AGGC    1

    
    U-UAUU    1

    
    U--AAC    1

    
    U--AAU    1

    
    U--CUC    1

    
    U--UAG    1

    
    U--UAU    1

    
    Omitted sequenced and counts

    
    ------   21

    
    -----C    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	96.55	34.97	1	1	Mini UNCG
2	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	89.66	35.02	2	1	Mini UNCG
3	Motif group HL_32346.4 View motif instance in 3D Basepair signature: cWW-F	82.76	26.67	2	1
4	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	82.76	18.43	3	2
5	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	75.86	21.22	3	2
6	Motif group HL_46501.1 View motif instance in 3D Basepair signature: cWW-cWS	62.07	5.29	3	1
7	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	58.62	24.21	2	1
8	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	58.62	8.93	3	1
9	Motif group HL_86870.2 View motif instance in 3D Basepair signature: cWW-F-F-F	51.72	-8.45	2	1
10	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	51.72	-41.21	3	2

Loop 2 Internal loop

Column numbers: 46-48, 113-114 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GUG*CC   39

    
    GCG*CC    1

    
    UUG*CC    1

    
    Omitted sequenced and counts

    
    ---*CC   10

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	98.21	2	0	Intercalated cWS
2	Motif group IL_89505.4 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	96.76	0	0	Single bulged U
3	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	96.70	2	0
4	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	94.96	0	0	Single stack bend
5	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	80.29	2	0
6	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	79.09	1	0	Single stack bend
7	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	68.51	3	0	Major groove platform
8	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	64.04	3	1	Multiple bulged bases
9	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	63.82	1	1	Major groove intercalation
10	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	52.75	2	0	Major groove platform

Loop 3 Internal loop

Column numbers: 51-57, 109-110 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GAACUAC*GC   30

    
    GAACUUC*GC    8

    
    GAACUAA*GC    2

    
    GAACCAC*GC    1

    
    -AACUAC*GC    1

    
    Omitted sequenced and counts

    
    -------*GC    9

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_88017.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R-L	100.00	88.36	0	0
2	Motif group IL_49714.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	100.00	87.54	0	0	Major groove intercalation
3	Motif group IL_46086.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	100.00	37.22	5	1
4	Motif group IL_25412.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	90.48	1.22	7	3	Major groove intercalation
5	Motif group IL_47087.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-cWW-tWH-L-L	71.43	2.25	2	2	Kink-turn related
6	Motif group IL_27393.10 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R-L-R	2.38	-14.82	5	3

Loop 4 Internal loop

Column numbers: 60-64, 101-106 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UCUUC*GUCGUG   23

    
    UCUUC*GUCGUA   17

    
    UCUUC*GUUGUA    2

    
    UCCUC*GUCGUA    1

    
    UCUUC*GUCGAA    1

    
    --UUC*GUCGAA    1

    
    --UUC*GUCGUA    1

    
    --UUC*GUUGUA    1

    
    Omitted sequenced and counts

    
    -----*GUCGUA    2

    
    -----*GUCGUG    1

    
    -----*----UG    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_56317.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW	93.62	14.33	4	3
2	Motif group IL_29223.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-cWW-cWW	38.30	-12.72	7	4
3	Motif group IL_70096.1 View motif instance in 3D Basepair signature: cWW-L-cWW-cWW	8.51	-3.50	5	3	Kink-turn related
4	Motif group IL_99498.1 View motif instance in 3D Basepair signature: cWW-L-R-tHW-cWW	6.38	-14.52	8	4
5	Motif group IL_07173.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	4.26	-53.38	6	3

Loop 5 Internal loop

Column numbers: 66-68, 97-99 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CGC*GAG   47

    
    Omitted sequenced and counts

    
    ---*GAG    2

    
    --C*GAG    1

    
    ---*---    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	89.98	1	0	Isolated non-canonical cWW pair
2	Motif group IL_44465.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	86.86	1	0	Isolated non-canonical cWW contact
3	Motif group IL_10167.6 View motif instance in 3D Basepair signature: cWW-cHW-cWW	100.00	79.00	1	0	Isolated cWH basepair
4	Motif group IL_14688.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	72.46	3	1	Isolated non-canonical cWW pair
5	Motif group IL_85599.2 View motif instance in 3D Basepair signature: cWW-tHS-cWW	100.00	66.84	3	0	Isolated tHS basepair with bulges
6	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	65.46	2	1
7	Motif group IL_57744.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	61.70	1	1	Isolated non-canonical cWW pair
8	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	50.54	1	1	Stack and bulge
9	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	45.12	1	1	Isolated cWS basepair
10	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	41.03	2	1	Multiple bulged bases

Loop 6 Internal loop

Column numbers: 69-73, 91-96 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AGAAA*UAGUAU   41

    
    GGAAA*UAGUAC    7

    
    Omitted sequenced and counts

    
    ----A*UAGUAU    1

    
    -----*UAGUAU    1

    
    -----*------    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_88269.4 View motif instance in 3D Basepair signature: cWW-tWW-cSH-tWH-tHS-cWW	100.00	87.99	3	1	6x5 Sarcin-Ricin; G-bulge
2	Motif group IL_21667.1 View motif instance in 3D Basepair signature: cWW-tSH-L-R-L-cWW	100.00	40.64	4	2
3	Motif group IL_62654.1 View motif instance in 3D Basepair signature: cWW-tSH-tHH-tHS-cWW	100.00	25.55	6	2	tSH-tHH-tHS
4	Motif group IL_42778.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-cWW	100.00	22.58	6	3
5	Motif group IL_97631.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tHS-cWW	100.00	22.12	5	3	Triple sheared related
6	Motif group IL_33886.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-R-L-R-cWW	100.00	20.81	6	3	Kink-turn with embedded cWW pair
7	Motif group IL_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	100.00	20.18	3	2	7x6 Sarcin-Ricin; G-bulge
8	Motif group IL_21001.1 View motif instance in 3D Basepair signature: cWW-L-R-tHW-L-cWW	100.00	18.41	5	2
9	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	100.00	12.15	4	2	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
10	Motif group IL_38862.4 View motif instance in 3D Basepair signature: cWW-cSH-R-tWH-tHS-cWW	100.00	4.18	4	1	5x5 Sarcin-Ricin with intercalated A; G-bulge

Loop 7 Hairpin loop

Column numbers: 78-86 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CUAGCCAUG   50

    
    Omitted sequenced and counts

    
    ---------    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_38808.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	47.82	4	2
2	Motif group HL_83632.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	100.00	9.46	2	2	tRNA anticodon loop

Loop 8 Internal loop

Column numbers: 134-136, 256-257 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GAG*CC   51

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	100.00	0	Single stack bend
2	Motif group IL_31462.6 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	100.00	0	Single bulged A
3	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	100.00	0	Single stack bend
4	Motif group IL_10569.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	99.41	2
5	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	96.85	2	Multiple bulged bases
6	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	93.80	1	Major groove intercalation
7	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	87.35	3
8	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	86.52	1	Stack and bulge
9	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	80.96	2	Major groove platform
10	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	75.28	3	Major groove platform

Loop 9 Internal loop

Column numbers: 137-140, 254-255 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CCAU*AG   51

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_22551.4 View motif instance in 3D Basepair signature: cWW-L-cWW-L	100.00	94.65	3	0
2	Motif group IL_95583.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	89.19	2	0	Minor groove platform, major groove intercalation
3	Motif group IL_82107.4 View motif instance in 3D Basepair signature: cWW-cWW	100.00	83.17	1	0	Multiple bulged bases
4	Motif group IL_42626.2 View motif instance in 3D Basepair signature: cWW-cWW	100.00	61.07	4	1
5	Motif group IL_15052.4 View motif instance in 3D Basepair signature: cWW-L-cWW-L	100.00	59.31	3	1	Minor groove platform
6	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	55.52	3	1
7	Motif group IL_73355.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L	100.00	50.15	3	1
8	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	48.19	5	1	Intercalated cWS
9	Motif group IL_68140.4 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	47.38	3	1	Major groove minor groove platform; mini C-loop
10	Motif group IL_00881.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L	100.00	45.85	3	1

Loop 10 Internal loop

Column numbers: 148-149, 244-246 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UG*CAA   27

    
    UG*CGA   23

    
    UU*CAA    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_48076.6 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	89.33	0	0	Major groove platform
2	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	88.29	2	0	Major groove intercalation
3	Motif group IL_10569.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	83.34	2	0
4	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	81.68	0	0	Single stack bend
5	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	75.92	0	0	Multiple bulged bases
6	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	75.77	2	0	Major groove platform
7	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	67.29	2	0	Single stack bend
8	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	67.17	3	1
9	Motif group IL_33761.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	64.86	2	0
10	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	62.21	3	1

Loop 11 4-way junction loop

Column numbers: 152-155, 170-171, 229-231, 240-241 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GAAC*GA*UUG*CC   51

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance
1	Motif group J4_47478.1 View motif instance in 3D Basepair signature: cWW-F-cWW-cWS-cHW-cWW-cWW	100.00	100.00	0	0
2	Motif group J4_69073.1 View motif instance in 3D Basepair signature: cWW-cHS-cWW-cWS-cHW-cWW-cWW	100.00	100.00	0	0
3	Motif group J4_57344.1 View motif instance in 3D Basepair signature: cWW-F-cWW-F-cWW-cSH-cWW	100.00	42.05	5	1

Loop 12 Hairpin loop

Column numbers: 160-165 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GAGUAC   51

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_49922.4 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	97.59	2	0
2	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	78.05	0	0
3	Motif group HL_38901.2 View motif instance in 3D Basepair signature: cWW-F-cSH	100.00	55.73	1	1	tRNA D-loop
4	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	100.00	50.22	1	1
5	Motif group HL_20811.4 View motif instance in 3D Basepair signature: cWW-cWS-F	100.00	46.86	4	2	tRNA D-loop
6	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	46.10	3	1
7	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	100.00	44.22	1	1
8	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	43.70	3	1
9	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	41.47	3	1
10	Motif group HL_56334.1 View motif instance in 3D Basepair signature: cWW-F	100.00	32.26	1	1	Mini UNCG

Loop 13 Internal loop

Column numbers: 173-176, 224-227 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UUGC*GAGA   30

    
    UCGC*GAAA   10

    
    UUGC*GCCA    7

    
    UUAC*GUCA    2

    
    UCCC*GGUA    1

    
    Omitted sequenced and counts

    
    UURC*GUCA    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_85033.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW-cWW	82.00	31.04	3	1	Tandem non-canonical cWW pairs
2	Motif group IL_25872.4 View motif instance in 3D Basepair signature: cWW-cWW-cWH-cWW	80.00	-2.70	2	1
3	Motif group IL_58112.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cWW	80.00	-7.90	4	2
4	Motif group IL_92446.2 View motif instance in 3D Basepair signature: cWW-cWW-R-L-L	74.00	22.42	5	1
5	Motif group IL_02203.1 View motif instance in 3D Basepair signature: cWW-cSW-cWW-cWW	60.00	-6.41	5	2
6	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	24.00	-39.26	4	2	Isolated non-canonical cWW pair
7	Motif group IL_99358.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	22.00	3.59	2	2
8	Motif group IL_69145.3 View motif instance in 3D Basepair signature: cWW-L-cWW-L-R-L-R-R	20.00	-17.14	3	3	Pseudoknot
9	Motif group IL_28564.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	20.00	-19.23	4	3
10	Motif group IL_70335.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	20.00	-21.43	7	4

Loop 14 Internal loop

Column numbers: 180-183, 215-220 - This loop does not map to nucleotides in a 3D structure with xyz coordinates.

    Scored sequences and counts

    
    GACG*CAAUGC   22

    
    GAUG*CAAUGC   10

    
    GAAG*CUAUGC    8

    
    GGUG*CAAUAC    4

    
    AAAG*CUAUGU    3

    
    GAAG*CUGUGC    1

    
    GACG*CCAUGC    1

    
    GACG*CUAUGC    1

    
    GUUG*CAAUGC    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_11344.2 View motif instance in 3D Basepair signature: cWW-cSS-L-cWW	96.08	12.18	3	3	180 degree turn
2	Motif group IL_05192.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW-L	92.16	34.11	5	2
3	Motif group IL_90346.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L-L	90.20	18.75	3	3
4	Motif group IL_69145.3 View motif instance in 3D Basepair signature: cWW-L-cWW-L-R-L-R-R	90.20	14.99	5	3	Pseudoknot
5	Motif group IL_96332.5 View motif instance in 3D Basepair signature: cWW-cWW-L-R-L-cWW-L	86.27	2.40	5	3
6	Motif group IL_25186.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-cWW	64.71	-4.75	6	3
7	Motif group IL_34737.1 View motif instance in 3D Basepair signature: cWW-L-cHW-L-cWW-L	23.53	-13.20	4	4
8	Motif group IL_29471.1 View motif instance in 3D Basepair signature: cWW-cWW-L-tHS-L-cWW	7.84	-58.42	6	5
9	Motif group IL_70096.1 View motif instance in 3D Basepair signature: cWW-L-cWW-cWW	1.96	-21.54	6	4	Kink-turn related
10	Motif group IL_68909.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW	1.96	-33.28	5	3

Loop 15 Internal loop

Column numbers: 184-186, 212-214 - This loop does not map to nucleotides in a 3D structure with xyz coordinates.

    Scored sequences and counts

    
    ACC*GCU   38

    
    ACU*ACU   11

    
    ACA*UCU    2

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	82.46	1	0	Isolated non-canonical cWW pair
2	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	78.61	2	0	Isolated non-canonical cWW pair
3	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	69.32	3	0	Stack and bulge
4	Motif group IL_28037.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	61.27	1	0	Isolated non-canonical cWW pair
5	Motif group IL_10796.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	53.74	4	0
6	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	51.74	3	1
7	Motif group IL_14688.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	41.34	3	1	Isolated non-canonical cWW pair
8	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	34.04	3	1	Isolated cWS basepair
9	Motif group IL_67095.2 View motif instance in 3D Basepair signature: cWW-tWW-cWW	100.00	31.79	3	1	Isolated tWW turn
10	Motif group IL_09990.4 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	100.00	22.68	1	1

Loop 16 Internal loop

Column numbers: 189-190, 203-209 - This loop does not map to nucleotides in a 3D structure with xyz coordinates.

    Scored sequences and counts

    
    GU*AU-AAAC   18

    
    GU*AUC-AAC   12

    
    GU*AUCAAAC    6

    
    GU*AUU-AAC    4

    
    GU*AAC-AAC    3

    
    GU*AACAAAC    1

    
    GU*AUCUAAC    1

    
    GU*AUUAAAC    1

    
    GU*AAC-CAC    1

    
    GU*AC-AAAC    1

    
    GU*AGC-AAC    1

    
    GU*AU-AACC    1

    
    GU*AUA-AAC    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_46086.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	72.55	7.90	6	2
2	Motif group IL_38186.6 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	62.75	21.77	5	1
3	Motif group IL_98347.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	45.10	-19.26	7	3
4	Motif group IL_25463.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	35.29	-21.79	5	3
5	Motif group IL_59302.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	33.33	-20.53	5	3
6	Motif group IL_33711.1 View motif instance in 3D Basepair signature: cWW-cSH-cWW-L-L-R-L	19.61	-17.96	4	4	Minor groove platform
7	Motif group IL_87211.1 View motif instance in 3D Basepair signature: cWW-cSW-L-cWW-L	15.69	-18.39	6	3
8	Motif group IL_41203.4 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R-cSH	15.69	-46.85	5	3	SSU/LSU pseudoknot
9	Motif group IL_49714.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	9.80	-16.00	5	3	Major groove intercalation
10	Motif group IL_14177.2 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	9.80	-32.27	5	3

Loop 17 Hairpin loop

Column numbers: 192-201 - This loop does not map to nucleotides in a 3D structure with xyz coordinates.

    Scored sequences and counts

    
    CUUUC--UUG   44

    
    CUUUCCAUUG    4

    
    CUUUC--GUG    2

    
    Omitted sequenced and counts

    
    CUUUY--UUG    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_78197.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	92.00	40.01	3	1
2	Motif group HL_28075.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	92.00	28.87	2	2
3	Motif group HL_26934.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	92.00	26.48	4	2
4	Motif group HL_31585.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	92.00	24.36	3	1	Purine riboswitch
5	Motif group HL_77082.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	92.00	20.58	3	1	Pseudoknot geometry
6	Motif group HL_25967.2 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F	92.00	6.09	4	2
7	Motif group HL_08510.1 View motif instance in 3D Basepair signature: cWW-F-F-cSH-F-F	88.00	4.17	4	2
8	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	88.00	0.78	1	1
9	Motif group HL_42046.2 View motif instance in 3D Basepair signature: cWW-tSS-F-F-F	88.00	-6.26	2	2
10	Motif group HL_38808.1 View motif instance in 3D Basepair signature: cWW-cWW	8.00	2.31	4	3

Loop 18 Hairpin loop

Column numbers: 233-238 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GCGUGC   50

    
    GCAUGC    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance
1	Motif group HL_81100.2 View motif instance in 3D Basepair signature: cWW	100.00	67.36	1	1
2	Motif group HL_48417.5 View motif instance in 3D Basepair signature: cWW-F-F	100.00	36.53	2	1
3	Motif group HL_86870.2 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	18.56	2	2
4	Motif group HL_65313.1 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	12.93	4	2
5	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	9.68	4	2
6	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	5.60	4	2
7	Motif group HL_37344.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	4.77	4	2
8	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	98.04	14.26	2	2
9	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	98.04	2.57	3	2
10	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	1.96	-8.54	3	3

Loop 19 Internal loop

Column numbers: 262-264, 287-289 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AGU*GGU   36

    
    AGC*GGU   15

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_44465.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	80.46	3	0	Isolated non-canonical cWW contact
2	Motif group IL_10167.6 View motif instance in 3D Basepair signature: cWW-cHW-cWW	100.00	73.93	2	0	Isolated cWH basepair
3	Motif group IL_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	47.86	2	0	Isolated non-canonical cWW pair
4	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	20.67	2	1	Isolated cWS basepair
5	Motif group IL_99358.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	29.41	4.24	3	1
6	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	29.41	1.29	5	2
7	Motif group IL_67095.2 View motif instance in 3D Basepair signature: cWW-tWW-cWW	29.41	0.28	5	2	Isolated tWW turn
8	Motif group IL_57744.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	29.41	-1.78	2	1	Isolated non-canonical cWW pair

Loop 20 Internal loop

Column numbers: 265-268, 283-286 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GUUG*UUGU   50

    
    GUUG*UUGC    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_02203.1 View motif instance in 3D Basepair signature: cWW-cSW-cWW-cWW	100.00	70.62	2	0
2	Motif group IL_85033.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW-cWW	100.00	14.43	3	1	Tandem non-canonical cWW pairs
3	Motif group IL_77658.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW-cWW	100.00	8.14	2	1	Tandem non-canonical cWW pairs
4	Motif group IL_81522.2 View motif instance in 3D Basepair signature: cWW-L-L-cWW	100.00	1.92	4	2	Major groove minor groove platform with intercalation; mini C-loop
5	Motif group IL_51479.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	1.96	-5.24	3	1
6	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	1.96	-16.24	2	1	Isolated non-canonical cWW pair

Loop 21 Hairpin loop

Column numbers: 272-279 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CGCGAAAG   35

    
    UGCGAAAG   14

    
    UGCGAACG    1

    
    Omitted sequenced and counts

    
    CGCSAAAG    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_81538.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F-F	98.00	35.38	1	1	GNRA with tandem sheared
2	Motif group HL_86769.4 View motif instance in 3D Basepair signature: cWW-cWW-cSH-F	98.00	20.39	4	2
3	Motif group HL_04259.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	72.00	12.83	3	2	GNRA with extra cWW
4	Motif group HL_10540.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	70.00	7.25	2	2
5	Motif group HL_00914.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	70.00	5.48	4	2
6	Motif group HL_50860.2 View motif instance in 3D Basepair signature: cWW-F-cWH-F-F-F-F	70.00	3.31	4	2
7	Motif group HL_93438.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	70.00	0.07	2	2
8	Motif group HL_93324.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	70.00	-0.58	2	2	Pseudoknot geometry
9	Motif group HL_41464.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	70.00	-2.52	5	3
10	Motif group HL_72628.1 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F-F	70.00	-4.45	3	3

Loop 22 Hairpin loop

Column numbers: 296-301 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UGAUAG   51

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	48.77	2	1
2	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	47.71	2	1
3	Motif group HL_04783.2 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	47.64	2	1
4	Motif group HL_62934.1 View motif instance in 3D Basepair signature: cWW-tSH-F	100.00	45.61	2	1
5	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	44.76	2	1	Pseudoknot geometry
6	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	100.00	44.61	2	1
7	Motif group HL_52953.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	44.53	3	1
8	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	39.27	2	1
9	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	100.00	23.28	2	1
10	Motif group HL_82710.2 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	23.11	3	1

Loop 23 Hairpin loop

Column numbers: 306-315 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CUUGCGAGUG   50

    
    CUUGCAAGUG    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_55436.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	100.00	49.28	4	2
2	Motif group HL_04171.7 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F-F-F-F	100.00	49.22	5	3
3	Motif group HL_99867.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	100.00	26.38	4	3
4	Motif group HL_87463.1 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F-F-F	100.00	25.31	5	3
5	Motif group HL_61996.2 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F	100.00	18.35	4	2
6	Motif group HL_98864.1 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F-F-F-F	100.00	15.86	5	3	T-loop with unstacked turn
7	Motif group HL_81545.2 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F-F	100.00	13.93	5	3
8	Motif group HL_29129.3 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F-F	98.04	11.08	5	3
9	Motif group HL_41543.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	98.04	8.85	5	3
10	Motif group HL_67079.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F	1.96	-12.53	6	4

Loop 24 Hairpin loop

Column numbers: 340-348 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CACCAUGAG   23

    
    CAUCAUGAG   17

    
    CAACAUGAG   10

    
    Omitted sequenced and counts

    
    SMACAUGAG    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_64690.6 View motif instance in 3D Basepair signature: cWW-cSW-F-F-F-F	100.00	39.02	4	2
2	Motif group HL_25847.2 View motif instance in 3D Basepair signature: cWW-F-cSH-tHW-F-F-F	100.00	15.95	5	3
3	Motif group HL_07951.3 View motif instance in 3D Basepair signature: cWW-F-F	100.00	5.67	3	3	tRNA D-loop
4	Motif group HL_80241.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F	54.00	10.36	4	2
5	Motif group HL_20743.5 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F-F	54.00	4.73	3	2
6	Motif group HL_80599.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F	34.00	-0.52	4	4
7	Motif group HL_20535.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	34.00	-1.83	5	3
8	Motif group HL_33983.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	34.00	-3.68	4	4
9	Motif group HL_15802.1 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F	34.00	-10.38	5	4
10	Motif group HL_18423.1 View motif instance in 3D Basepair signature: cWW-tSH-tHS-F	34.00	-16.89	4	3