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 RF00209, RF00061 .
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: 8-15
Loop 2IL Column numbers: 51-57, 109-110
Loop 3IL Column numbers: 60-64, 101-106
Loop 4IL Column numbers: 66-68, 97-99
Loop 5IL Column numbers: 69-74, 90-96
Loop 6HL Column numbers: 78-86
Loop 7IL Column numbers: 120-122, 132-134
Loop 8HL Column numbers: 124-130
Loop 9IL Column numbers: 148-149, 244-246
Loop 10J4 Column numbers: 152-155, 170-171, 229-231, 240-241
Loop 11HL Column numbers: 160-165
Loop 12IL Column numbers: 180-186, 212-220
Loop 13IL Column numbers: 190-191, 202-208
Loop 14HL Column numbers: 192-201
Loop 15HL Column numbers: 233-238
Loop 16IL Column numbers: 257-263, 274-279
Loop 17HL Column numbers: 265-272
Loop 18IL Column numbers: 297-301, 318-319
Loop 19HL Column numbers: 307-312
Loop 20HL Column numbers: 327-333
Loop 21HL Column numbers: 340-348
Loop 22HL Column numbers: 353-354

Loop 1 Hairpin loop

Column numbers: 8-15 - This loop does not map to nucleotides in a 3D structure with xyz coordinates.

    Scored sequences and counts

    
    CCUGAUGG    7

    
    CU-AAUAG    3

    
    CU--UUCG    3

    
    CU-UAACG    2

    
    UC-UAUGA    2

    
    C--UAAUG    2

    
    CU--UACG    2

    
    CCGAUUGG    1

    
    CU-UAUUG    1

    
    GG-AGGCG    1

    
    CU--AACG    1

    
    CU--AAUG    1

    
    CU--CUCG    1

    
    CU--UAGG    1

    
    CU--UAUG    1

    
    ------CG    1

    
    Omitted sequenced and counts

    
    --------   21

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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_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	60.00	-360.74	2.5	2.5
2	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	60.00	-371.40	3	2
3	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	60.00	-372.63	3	2
4	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	56.67	-369.18	3	2
5	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	50.00	-373.23	2	2
6	Motif group HL_20535.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	43.33	-371.24	4	3
7	Motif group HL_48778.2 View motif instance in 3D Basepair signature: cWW-F	43.33	-419.12	2	2	Mini UNCG
8	Motif group HL_46501.1 View motif instance in 3D Basepair signature: cWW-cWS	40.00	-48.39	2	2
9	Motif group HL_43517.1 View motif instance in 3D Basepair signature: cWW-F-F-F	40.00	-384.84	3	2
10	Motif group HL_49922.4 View motif instance in 3D Basepair signature: cWW-F-F-F	40.00	-396.05	2	1

Loop 2 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

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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_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 3 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

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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_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 4 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

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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	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 5 Internal loop

Column numbers: 69-74, 90-96 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AGAAAG*UUAGUAU   41

    
    GGAAAG*UUAGUAC    7

    
    ----AG*UUAGUAU    1

    
    Omitted sequenced and counts

    
    ------*UUAGUAU    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_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	97.96	88.92	3	0	7x6 Sarcin-Ricin; G-bulge
2	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	97.96	47.75	4	1	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
3	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	97.96	27.26	5	2	8x6 Sarcin-Ricin with inserted A; G-bulge
4	Motif group IL_16458.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-cSH-tWH-tHS-cWW	97.96	22.90	4	2	Sarcin-Ricin target in LSU H95; G-bulge
5	Motif group IL_41756.4 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW-L	97.96	7.58	5	2	8x6 Sarcin-Ricin with inserted Y; G-bulge
6	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	97.96	0.78	4	2	8x7 Sarcin-Ricin; G-bulge

Loop 6 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 7 Internal loop

Column numbers: 120-122, 132-134 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CCC*GAG   50

    
    UCC*GAG    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_67095.2 View motif instance in 3D Basepair signature: cWW-tWW-cWW	100.00	98.18	2	0	Isolated tWW turn
2	Motif group IL_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	95.73	0	0	Isolated non-canonical cWW pair
3	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	77.05	2	0	Isolated cWS basepair
4	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	71.25	3	1
5	Motif group IL_57744.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	67.16	2	0	Isolated non-canonical cWW pair
6	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	63.68	1	1	Isolated non-canonical cWW pair
7	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	57.64	1	1	Stack and bulge
8	Motif group IL_28037.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	49.89	2	1	Isolated non-canonical cWW pair
9	Motif group IL_14688.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	44.73	3	1	Isolated non-canonical cWW pair
10	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	40.73	3	1	Multiple bulged bases

Loop 8 Hairpin loop

Column numbers: 124-130 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CCUCCCG   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_08100.1 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	26.79	1	1
2	Motif group HL_10453.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	100.00	25.79	4	2	tRNA anticodon loop
3	Motif group HL_47787.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	13.46	1	1
4	Motif group HL_80362.1 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	9.11	2	2
5	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	100.00	3.65	2	2
6	Motif group HL_13189.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	2.10	2	2

Loop 9 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 10 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

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
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 11 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 12 Internal loop

Column numbers: 180-186, 212-220 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GACGACC*GCUCAAUGC   20

    
    GAUGACC*GCUCAAUGC   10

    
    GAAGACU*ACUCUAUGC    7

    
    GGUGACC*GCUCAAUAC    4

    
    AAAGACU*ACUCUAUGU    3

    
    GACGACA*UCUCAAUGC    2

    
    GAAGACC*GCUCUAUGC    1

    
    GAAGACU*ACUCUGUGC    1

    
    GACGACC*GCUCCAUGC    1

    
    GACGACC*GCUCUAUGC    1

    
    GUUGACC*GCUCAAUGC    1

No Matches Found View All Results for this Loop

Loop 13 Internal loop

Column numbers: 190-191, 202-208 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UC*GAU-AAA   18

    
    UC*GAUC-AA   12

    
    UC*GAUCAAA    6

    
    UC*GAUU-AA    4

    
    UC*GAAC-AA    3

    
    UC*GAACAAA    1

    
    UC*GAUCUAA    1

    
    UC*GAUUAAA    1

    
    UC*GAAC-CA    1

    
    UC*GAC-AAA    1

    
    UC*GAGC-AA    1

    
    UC*GAU-AAC    1

    
    UC*GAUA-AA    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_87211.1 View motif instance in 3D Basepair signature: cWW-cSW-L-cWW-L	94.12	35.56	4	1
2	Motif group IL_46086.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	92.16	20.59	5	2
3	Motif group IL_25412.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	84.31	0.37	7	3	Major groove intercalation
4	Motif group IL_59302.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW-L	70.59	-3.44	6	2
5	Motif group IL_88017.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R-L	58.82	2.14	4	2
6	Motif group IL_49714.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	56.86	-0.18	4	2	Major groove intercalation
7	Motif group IL_38186.6 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L-R	50.98	-15.10	2	2
8	Motif group IL_98347.1 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	45.10	-17.64	3	3
9	Motif group IL_25573.1 View motif instance in 3D Basepair signature: cWW-tSW-L-cWW-L-L	39.22	-15.77	5	3
10	Motif group IL_14177.2 View motif instance in 3D Basepair signature: cWW-L-R-L-cWW	37.25	-29.82	6	3

Loop 14 Hairpin loop

Column numbers: 192-201 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CUUUC--UUG   44

    
    CUUUCCAUUG    4

    
    CUUUC--GUG    2

    
    Omitted sequenced and counts

    
    CUUUY--UUG    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_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 15 Hairpin loop

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

    Scored sequences and counts

    
    GCGUGC   50

    
    GCAUGC    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
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 16 Internal loop

Column numbers: 257-263, 274-279 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CGAGUAG*CGAAAG   49

    
    CUAGUAG*CGAACG    1

    
    Omitted sequenced and counts

    
    CGAGUAG*CSAAAG    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_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	100.00	99.97	1	0	7x6 Sarcin-Ricin; G-bulge
2	Motif group IL_24254.1 View motif instance in 3D Basepair signature: cWW-cWW-tHH-cSH-tWH-tHS-cWW	100.00	42.57	6	2	7x6 Sarcin-Ricin with UU cWW pair; G-bulge
3	Motif group IL_41756.4 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW-L	100.00	41.22	4	1	8x6 Sarcin-Ricin with inserted Y; G-bulge
4	Motif group IL_47346.2 View motif instance in 3D Basepair signature: cWW-tSH-L-R-tHH-tHS-cWW	100.00	29.89	4	2	tSH-tSH-tHH-tHS
5	Motif group IL_04346.10 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW	100.00	22.04	3	2	8x7 Sarcin-Ricin; G-bulge
6	Motif group IL_61286.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-tWH-L-tHS-cWW	100.00	20.13	5	3	8x6 Sarcin-Ricin with inserted A; G-bulge
7	Motif group IL_16458.4 View motif instance in 3D Basepair signature: cWW-L-R-L-R-cSH-tWH-tHS-cWW	100.00	5.22	5	3	Sarcin-Ricin target in LSU H95; G-bulge
8	Motif group IL_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	98.00	35.06	4	2	8x6 Sarcin-Ricin with bulged A; G-bulge
9	Motif group IL_29198.2 View motif instance in 3D Basepair signature: cWW-cWW-L-R-cSH-R-tWH-tHS-cWW	98.00	27.28	4	2	7x7 Sarcin-Ricin with intercalated A; G-bulge
10	Motif group IL_65594.1 View motif instance in 3D Basepair signature: cWW-L-R-tSW-tHH-cSH-tWH-tHS-cWW	2.00	-8.69	5	4	8x7 Sarcin-Ricin; G-bulge

Loop 17 Hairpin loop

Column numbers: 265-272 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GUUGGGUC   36

    
    GUUGGGUU   15

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_77436.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	100.00	38.49	2	1	T-loop related
2	Motif group HL_21372.1 View motif instance in 3D Basepair signature: cWW-F-cSH-F-F	100.00	9.93	4	2
3	Motif group HL_27670.2 View motif instance in 3D Basepair signature: cWW-tWH-F-F	70.59	11.18	2	2	T-loop with unstacked turn
4	Motif group HL_09452.1 View motif instance in 3D Basepair signature: cWW-F-F-F	70.59	7.53	3	3
5	Motif group HL_22622.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	70.59	2.95	5	3
6	Motif group HL_57863.1 View motif instance in 3D Basepair signature: cWW-F-F-cWH-cWH-F	70.59	-1.33	3	3	G-quadruplex fragment
7	Motif group HL_20535.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	70.59	-3.08	3	3
8	Motif group HL_01609.3 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F	70.59	-3.10	3	2	T-loop with 2 bulged bases not stacked
9	Motif group HL_86012.1 View motif instance in 3D Basepair signature: cWW-tWH-F-F-F-F	70.59	-6.34	3	3	T-loop with unstacked turn

Loop 18 Internal loop

Column numbers: 297-301, 318-319 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    GAUAG*CC   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 IL_47078.3 View motif instance in 3D Basepair signature: cWW-cWS-L-cWW-L	100.00	44.10	3	1	Minor groove platform
2	Motif group IL_00881.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L	100.00	42.93	4	1
3	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	37.71	2	1
4	Motif group IL_25463.1 View motif instance in 3D Basepair signature: cWW-L-cWW-L-L	100.00	31.99	5	2
5	Motif group IL_42626.2 View motif instance in 3D Basepair signature: cWW-cWW	100.00	29.33	2	1
6	Motif group IL_15052.4 View motif instance in 3D Basepair signature: cWW-L-cWW-L	100.00	26.76	1	1	Minor groove platform
7	Motif group IL_87211.1 View motif instance in 3D Basepair signature: cWW-cSW-L-cWW-L	100.00	20.37	4	1
8	Motif group IL_68140.4 View motif instance in 3D Basepair signature: cWW-cSH-cWW	100.00	20.22	1	1	Major groove minor groove platform; mini C-loop
9	Motif group IL_81522.2 View motif instance in 3D Basepair signature: cWW-L-L-cWW	100.00	16.97	5	2	Major groove minor groove platform with intercalation; mini C-loop
10	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	15.84	1	1	Major groove intercalation

Loop 19 Hairpin loop

Column numbers: 307-312 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    UUGCGA   50

    
    UUGCAA    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
1	Motif group HL_99040.1 View motif instance in 3D Basepair signature: F-F-F-F-F-F	100.00	73.17	1	0
2	Motif group HL_50006.2 View motif instance in 3D Basepair signature: cWW-F-F	100.00	53.63	3	1
3	Motif group HL_56131.2 View motif instance in 3D Basepair signature: cWW-F-F	100.00	36.04	1	1
4	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	100.00	20.38	3	2
5	Motif group HL_93535.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	8.12	4	2
6	Motif group HL_46501.1 View motif instance in 3D Basepair signature: cWW-cWS	100.00	5.70	4	2
7	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	100.00	4.96	3	2
8	Motif group HL_43517.1 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	0.24	3	2
9	Motif group HL_56676.1 View motif instance in 3D Basepair signature: cWW-F-F	98.04	50.86	3	1
10	Motif group HL_32392.1 View motif instance in 3D Basepair signature: cWW-F-F	98.04	43.23	1	1

Loop 20 Hairpin loop

Column numbers: 327-333 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    CUCGUAG   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 HL_66103.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	25.28	2	2
2	Motif group HL_86769.4 View motif instance in 3D Basepair signature: cWW-cWW-cSH-F	100.00	19.74	3	2
3	Motif group HL_31585.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	100.00	15.18	2	2	Purine riboswitch
4	Motif group HL_62934.1 View motif instance in 3D Basepair signature: cWW-tSH-F	100.00	10.98	2	2
5	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	100.00	7.66	4	2
6	Motif group HL_50537.6 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	6.73	3	3	tRNA anticodon loop with synthetase
7	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	100.00	5.48	3	2
8	Motif group HL_21372.1 View motif instance in 3D Basepair signature: cWW-F-cSH-F-F	100.00	0.77	4	2

Loop 21 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

Loop 22 Hairpin loop

Column numbers: 353-354 - View nucleotides in PDB file(s)

    Scored sequences and counts

    
    AA   31

    
    CU   18

    
    GA    1

    
    UC    1

No Matches Found View All Results for this Loop

Nucleotide numbers Coloring options:

JAR3D Query RF00061-CCF-3.98 completed Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF00061 Hepatitis C virus internal ribosome entry site

Input Summary

Jump to results for:

Loop 1 Hairpin loop

Loop 2 Internal loop

Loop 3 Internal loop

Loop 4 Internal loop

Loop 5 Internal loop

Loop 6 Hairpin loop

Loop 7 Internal loop

Loop 8 Hairpin loop

Loop 9 Internal loop

Loop 10 4-way junction loop

Loop 11 Hairpin loop

Loop 12 Internal loop

Loop 13 Internal loop

Loop 14 Hairpin loop

Loop 15 Hairpin loop

Loop 16 Internal loop

Loop 17 Hairpin loop

Loop 18 Internal loop

Loop 19 Hairpin loop

Loop 20 Hairpin loop

Loop 21 Hairpin loop

Loop 22 Hairpin loop

JAR3D Query RF00061-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.