# STOCKHOLM 1.0
#=GF ID HCV_J7880
#=GF AC RF04309
#=GF DE Hepatitis C virus J7880 RNA
#=GF AU Marz M; 0000-0003-4783-8823
#=GF GA 90.0
#=GF NC 40.1
#=GF TC 93.3
#=GF SE Kevin Lamkiewicz; Sandra Triebel; Manja Marz;
#=GF SS Predicted; BM VeGETA v. 0.4, LocARNA 2.0.0RC8, RNAfold
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 25775547
#=GF RT Functionally conserved architecture of hepatitis C virus RNA genomes.
#=GF RA Mauger DM, Golden M, Yamane D, Williford S, Lemon SM, Martin DP, Weeks KM
#=GF RL Proc Natl Acad Sci U S A. 2015;112:3692-3697.
#=GF CC multi-loop in the coding region of the NS5B gene of HCV involved in
#=GF CC regulating rate replication [1]
#=GF WK Hepatitis_C_virus
#=GF SQ 57

NC_038882.1/7812-7934 GUCAAAGCAGCGGCGUCAAAAGUGAAGGCUAACUUGCUAUCCGUAGAGGAAGCUUGCAGCCUGACGCCCCCACAUUCAGCCAAAUCCAAGUUUGGCUAUGGGGCAAAAGACGUCCGUUGCCAU
NC_004102.1/7812-7934 GUCAAAGCAGCGGCGUCAAAAGUGAAGGCUAACUUGCUAUCCGUAGAGGAAGCUUGCAGCCUGACGCCCCCACAUUCAGCCAAAUCCAAGUUUGGCUAUGGGGCAAAAGACGUCCGUUGCCAU
EU234065.2/7707-7829  GUUAAAGCAGCGGCGUCGAAAGUGAAGGCUAACUUGCUAUCCGUAGAGGAAGCUUGCAGCCUGACGCCCCCACAUUCAGCCAGAUCCAAGUUUGGCUAUGGGGCAAAAGACGUCCGUUGCCAU
MN164851.1/7471-7593  AUCAAGGCAAAGGCAUCCACGGUGAAGGCGAGACUACUGACUGUAGAGGAGGCCUGCAAACUAACGCCCCCACAUUCGGCCAGAUCCAAAUUUGGCUAUGGGGCGAAGGAUGUCCGGAGCCUA
KJ439777.1/7812-7934  GUUAAGGCUAAGGCGUCAACAGUGAAGGCUAAACUGCUAUCUGUAGAGGAAGCUUGUAGCCUGACGCCCCCCCAUUCAGCCAGAUCUAAAUUUGGCUACGGGGCAAAGGACGUCCGAAGCCAC
MN977327.1/7762-7884  AUAAAGGCAAAGGCGUCCACAGUGAAGGCGAACCUGCUAUCCGUCGAGGAGGCAUGUGCCCUGACGCCCCCACAUUCGGCCAGAUCAAAAUUUGGCUAUGGGGCGAAGGACGUCCGGAGCCUU
AY587845.1/7748-7870  AUGAAGGCAAAGGCGUCCACAGUCAAGGCCAAACUUCUAUCCGUGGAAGAAGCCUGCAAGCUGACGCCCCCACAUUCGGCCAGAUCUAAAUUUGGCUAUGGGGCGAAGGACGUCCGGAACCUA
AJ851228.1/7785-7907  GCAAAGGCGAAGGCGUCCACAGUGAAGGCGGAACUGCUAUCCGUAGAGGAAGCGUGCCGCCUGACGCCCCCACACUCGGCCAAGUCCAAAUUUGGCUAUGGGGCAAAGGACGUCCGGAGCCUG
KY348757.1/7772-7894  GCUAAGGCGAAGGCAUCCACAGUGAAGGCUAAGCUGCUAUCCAUCGAGGAAGCUUGCCAACUGACGCCCCCACAUUCGGCCAAAUCCAAGUUUGGCUAUGGGGCGAAAGAUGUCCGGAGCCUA
KJ439768.1/7809-7931  AUUAAGGCGAAGGCGUCCACAGUGAAGGCCAGGCUACUCUCAGUGGAGGAAGCUUGCAGCCUGACGCCCCCGCACUCGGCUAAAUCCAAGUUCGGGUACGGGGCGAAGGACGUCCGGAGCCUA
MN164872.1/7471-7593  GCUAAGGCCAAGGCAUCCACUGUGAAGGCAGACUUGCUAUCCGUCGAGGAGGCUUGUAGCCUGACGCCCCCCCACUCGGCCAGAUCAAAAUUUGGCUACGGGGCGAAGGAUGUCCGAAGCCAU
MW689980.1/7616-7738  GCUAAGGCUAAGGCAUCCACAGUGAAGGCCGACUUGCUAUCCGUAGAGGAUGCAUGCGACCUGACGCCCCCCCACUCAGCCAGAUCAAAAUUUGGCUACGGGGCGAAGGAUGUCCGAAGCCAU
MW689962.1/7616-7738  GUUAAAGCAGCGGCGUCAAAAGUGAAGGCUAACUUGCUCUCCGUCGAGGAAGCAUGUAGCCUGACGCCCCCGCACUCAGCCAGAUCUAAGUUUGGGUUUGGGGCGAAGGAUGUCCGAAGCCAU
KX767023.1/7741-7863  AUGAAGGCGAAGGCGUCCACAGUGAAGGCUAGACUUCUAUCUGUAGAAGAAGCCUGCAAGCUGACACCCCCACAUUCGGCCAGAUCUAAAUUUGGCUAUGGGGCAAAGGACGUCCGGAGCCUA
EU234061.2/7757-7879  AUGAAGGCGAAGGCGUCCACAGUUAAGGCUAAACUUCUAUCCGUAGAAGAAGCCUGCAAGCUGACACCCCCACAUUCGGCCAAAUCCAAAUUUGGCUAUGGGGCAAAGGACGUCCGGAGCCUA
AB677533.1/7821-7943  AUGAAGGCGAAGGCGUCCACAGUUAAGGCUAAACUUCUAUCUAUAGAAGAAGCCUGCAAGCUGACGCCCCCACAUUCGGCCAAAUCCAAGUUUGGCUAUGGGGCAAAGGACGUCCGGAACCUA
MW689975.1/7800-7922  AUGAAGGCGAAGGCAUCCACAGUGAAGGCCAACAUGCUAUCCAUCGAGGAAGCUUGUAGCCUGACGCCCCCCCACUCUGCCAAAUCUAAGUUUGGCUAUGGGGCAAAGGAUGUCCGGAGCCAU
MW689965.1/7816-7938  GUUAAGGCAAAGGCGUCCACAGUGAAGGCCAGAUUGCUACCCAUAGAGGAAGCUUGUGGCCUGACGCCCCCACACUCAGCCAGAUCCAAAUUUGGCUAUGGGGCAAAGGACGUCCGGAGCCUA
MW689971.1/7772-7894  AUUAAGGCAAAGGCGUCCACAGUGAAGGCCAGGCUAUUGUCCGUAGAGGAAGCCUGUAGCCUGACGCCCCCACACUCGGCCAGAUCCAAAUUUGGCUAUGGGGCACAGGACGUCCGGAGCCUA
MW690013.1/7795-7917  GCAAAGGCUAAGGCGUCCACAGUGAAGGCUAACUUGCUAUCCGUAGAGGAAGCUUGCAGCCUGACGCCCCCCCACUCAGCCAGAUCAAAAUUUGGCUAUGGGGCGAAGGACGUCCGAAGCCAU
KC248199.1/7815-7937  GCUAAGGCGAAGGCAUCCACCGUGAAGGCGAGGCUCCUCUCCGUAGAAGAAGCUUGCCGCUUAACACCCCCCCACUCCGCCAGAUCUAAAUUUGGCUAUGGGGCGAAGGAUGUCCGGGACCUA
MN164860.1/7489-7611  GCAAAGGUCAAGGCGUCUACUGUGAAGGCAGACAUGCUCUCCGUGGAGGAAGCGUGCGACCUGACGCCCCCCCAUUCAGCCAAAUCUAAAUUUGGCUACGGGGCGAAAGACGUCCGCAACCAU
NC_009823.1/7877-7999 AUUAAGCUAGCGGCCUCCAAGGUCACCGCAAGGCUCCUCACCAUGGAGGAGGCUUGCCAGUUAACCCCACCCCAUUCUGCAAGAUCUAAAUAUGGGUUUGGGGCUAAGGAGGUCCGCAGCUUG
AF169004.1/7877-7999  AUCAAGCUAGCGGCUUCCAAGGUUAGUGCAAGGCUCCUCACCGUGGAGGAGGCGUGCCAGCUUACUCCACCCCAUUCUGCAAAAUCCAAGUAUGGGUUUGGAGCUAAGGAGGUCCGCAGCUUG
JX227965.1/7800-7922  GUCAAGCAGGCAGCCUCCACGGUUAGCGCUAAGCUCCUCUCCAUCGAGGAGGCGUGUGCGCUGACCCCGCCCCAUUCCGCUAGAUCAAAGUACGGUUUUGGGGCGAAAGAGGUUCGCAGCUUG
KC197233.1/7850-7972  AUUAAGCUAGCUGCCUCCACGGUUAGCGCCAGGCUUCUCACGAUCGAGGAAGCAUGCGCGCUGACCCCUCCCCAUUCCGCUAGAUCAAAAUACGGAUUCGGGGCAAAGGAGGUUCGCAGCUUA
AB047639.1/7877-7999  AUCAAGCUAGCGGCUUCCAAGGUCAGCGCAAGGCUCCUCACCUUGGAGGAGGCGUGCCAGUUGACUCCACCCCAUUCUGCAAGAUCCAAGUAUGGAUUCGGGGCCAAGGAGGUCCGCAGCUUG
MK548369.1/7804-7926  GUUAAGGCAGCGGCGUCAAMRGUGAAGGCUAACUUGCUAUCCGUAGAGGAAGCUUGCAGCCUGACGCCCCCACAYUCAGCCAGAUCCAAGUUUGGCUAUGGGGCUAAAGACGUCCGUUGCCAU
AY232740.1/7841-7963  GUUAAGCGGGCCGCCUCUAAGGUUAGUGCGAGGCUCCUCUCAGUAGAGGAAGCCUGCGCGCUGACCCCGCCCCACUCCGCCAAAUCACGGUACGGAUUUGGGGCAAAGGAGGUGCGCAGCUUA
KC197230.1/7853-7975  GUCAAGCUUGCCGCCUCCAAGGUCAGCGCCAGGCUUCUUUCGGUGGAAGAGGCAUGCAUGCUAACACCGCCCCAUUCUGCACGUUCCAAGUACGGAUUUGGGGCGAAGGAGGUCCGCAGCUUG
NC_009824.1/7840-7962 GUAAAGGAGCGAGCGUCUAGGGUAAAGGCUCGCAUGCUCACCAUCGAGGAAGCGUGCGCGCUCGUCCCUCCUCACUCUGCCCGAUCGAAGUUCGGGUAUAGUGCGAAGGACGUUCGCUCCUUG
KY620603.1/7839-7961  GUAAAGGAGCGAGCGUCUAAGGUAAAGGCCCGCAUGCUCACCAUCGAGGAAGCGUGCGCGCUCGUCCCUCCUCACUCUGCCCGGUCAAAGUUCGGGUAUAGUGCGAAGGACGUUCGCUCCUUG
KJ470619.1/7841-7963  GUGAAGGAGMGAGCGUCCAGGGUAAAGGCGCGUUUGCUUUCUAUUGAGGAAGCRAGCGCCCUUGUCCCCCCUCACUCGGCCCGAUCAAAGUUCGGGUACACUGCGAGGGACGUUCGCUCCUUG
JF735124.1/7840-7962  GURAGGGAGCUAGCGUCGGGAGUGCAGGCAGACUUGCUUUCUGUAGAGGAAGCUUGUAGCCUCACUCCCCCUCAUUCAGCCCGUUCCAAGUAUGGAUACGGGGCAAAAGAGGUGCGCUCCCUA
MN628597.1/7843-7965  GUAAAGGAGCGAGCGUCUAGGGUAAAGGCUCGCAUGCUCUCCAUCGAGGAAGCGUGCGCGCUCGUCCCCCCUCACUCUGCCCGGUCGAAGUUCGGGUAUAGUGCUAAGGACGUUCGCUCCUUG
KY620874.1/7851-7973  GUGAAGGAGCGAGCAUCGGGGGUGAAGGGUCGCCUACUCUCUUUCGAGGAAGCGUGCUCCCUUGUUCCCCCCCACUCUGCCCGGUCAAAGUACGGGUACAGUGCAAAGGAUGUUCGUUCCUUC
JF735122.1/7834-7956  AUUAAGGAAUUAGCAUCUGGGGURAAGGCYGAGCUACUCUCUGUWGAAGAAGCAUGCCGCCUUGUCCCCCCUCACUCCGCCAAAUCAAAAUUUGGCUAUGGAGCGAAGGAGGUGCGGUCCUUG
NC_009825.1/7741-7863 AUAAAGGCACGAGCAUCCAGAGUGAAGCCACGCUUGCUUACCACAGAGGAAGCUUGCGACCUGACGCCCCCCCACUCAGCCAGAUCAAAGUUCGGCUACGGGAAAAAGGAUGUUCGGAGCCAU
KM043284.1/7802-7924  AUCAAGGCGCGAGCAUCCAGAGUGAAGGCACGCUUGCUUACCGCAGAGGAAGCUUGCGACCUGACGCCCCCCCACUCUGCCAGAUCAAAAUUUGGCUAUGGGGCAAAGGAUGUUCGCAGCCAU
FJ462437.1/7796-7918  AUUAAGGCACAAGCCUCCACAGUGAAGGCGCGGUUACUCACGGUUGAGGAAGCCUGCAACCUGACGCCCCCCCACUCGGCCAGAUCAAAAUUUGGUUACGGGGCGAAGGAGGUUCGGAGCCAU
NC_009826.1/7759-7881 AUGAAGCGAUUAGCCUCCAAGGUUAAGGCCAGACUACUGCCCCUAGAGGAAGCCUGUGGGUUAACACCACCCCACUCCGCCCGUUCCAAGUACGGAUACGGCGCGAAGGAAGUUCGCUCUCUC
MH427311.1/7819-7941  AUGAAGCGACUAGCCUCCAAAGUUAAAGCCAGACUGCUGCCUCUCGAGGAAGCUUGUGGGUUAACACCACCCCAUUCCGCCCGUUCCAAGUAUGGAUACGGCGCUAAGGAGGUUCGCUCUCUC
DQ278891.1/7823-7945  GUUAAGGCCCGGGCCUCAGAGGUAACGGCUAAGCUCCUCUCAGUUGAGGAGGCAUGUGCCCUUACCCCUCCACACUCUGCUCGUUCGAAGUUCGGGUAUGGAGCGAAAGAUGUCCGGAGUCAU
LC435023.1/7774-7896  GUGAAGGAUCGGGCUUCUAGUGUGAGUGCCAGGCUCCUCUCAACGGAGGAAGCCUGCAAACUCACCCCCCCUCACUCGGCUCGCUCCAAGUUCGGGUACGGGGCUAAGGAAGUCCGAAGCCUU
MK327987.1/7821-7943  GUAAAGCUGCGAGCGUCCGGCGUAAAGGCAAAGCUCCUCAGCAUUGAGGAAGCGUGCGACCUCACACCAGCACACUCAGCCCGCUCCAAAUUCGGAUACGGCGCCAAGGACGUUCGCAGCCAU
MG878999.1/7492-7614  AUAAAGCUCCGGGCCUCCAAGGUGGACGCCAGGCUACUCACAACUGAGGAAGCCUGUGACCUAACACCCCCAAAGUCGGCUCGAUCAAAGUUCGGCUAUGGGGCCAAGGACGUCCGAGAGCAU
KC844040.1/7827-7949  AUAAAACUCCGGGCUUCGGAGGUGGAAGCGAGGCUACUCACAGUUGAGGAAGCCUGCGAUUUAACCCCUCCGCACUCUGCCCGUUCCAAGUACGGGUAYGGCGCAAAGGAAGUCCGGAGUCAU
MG717928.1/7840-7962  AUUAAGCUUCGAGCGUCCAAGGUGCAGGCGAAGCUCUUAUCCGUAGAGGAAGCCUGCGACCUCACACCAUCGCACUCAGCCCGGUCCAAAUAUGGGUAUGGUGCACAGGACGUUAGAAGCCAU
KJ678751.1/7794-7916  AUCAAGCUUCGAGCGUCCACGGUGCAGGCGAAGCUCCUAUCCAUAGAGGAAGCCUGCGACCUCACACCAUCGCACUCAGCCCGGUCCAAAUAUGGGUAUAGUGCACAGGACGUUAGAAGCCAU
MG717925.1/7780-7902  AUUAAGCUUCGAGCGUCCUCGGUGCAGGCGAAGCUCCUAUCCAUAGAGGAAGCCUGCGACCUCACACCAUCGCAUUCAGCCCGGUCCAAAUAUGGGUAUGGUGCACAGGACGUUAGAAGCCAU
NC_009827.1/7837-7959 AUUAAGCUCAGAGCAUCGACCGUGCACGCCAGGCUCCUAUCCACCGAGGAGGCCUGUUCGCUCACUCCACCGCACUCAGCCCGAUCAAGGUAUGGGUAUGGAGCACGGGAUGUUAGGAGCCAU
AY878652.1/7791-7913  GUCAAACUCCGGGCGUCGCAGGUGACGGCAAAGCUCCUCUCUAUUGAGGAUGCCUGCGACCUCACCCCCCCACACUCGGCUCGCUCAAAGUUUGGGUAUGGGGCAAAAGAUGUCCGGAGUCAU
KM504115.1/7825-7947  AUCAAAGCCCGGGCUUCCGGGGUGAGUGCUAGACUCCUCUCCACGGAGGAGGCAUGCAGCCUCACACCCCCGCAUUCAGCCCGAUCCAAGUUCGGGUACGGGGCGAAGGAAGUCCGGAGCCAU
EU158186.1/7793-7915  AUCAAGCUCCGUGCGUCCACGGUGACUGCAAGGCUCCUCUCAGUGGAGGAAGCCUGCGACCUCACUCCUCCCCAUUCCGCCCGUUCAAAGUUCGGGUAUGGGGCGAAGGACGUUAGGAGCCAU
MK139017.1/7824-7946  GUUAAGCUCCGAGCAUCUCAAGUGACGGCUAGGCUCCUCCCCGUUGAGGAAGCCUGUGACCUCACCCCCCCACACUCAGCUCGUUCAAAGUUUGGGUACGGGGCAAAGGAUGUCCGGAGUCAU
NC_030791.1/7816-7938 GUGAAAGCGGAUGCUUCCACGGUUAAGGCGCAGUUGCUCUCAGUAGAGGAAGCUGCUGCCCUCACCCCUGCCCACUCAGCCAGAUCUAAGUUUGGGUACGGGGCAAAGGAAGUCAGAUCUCUU
MH590700.1/7825-7947  GUGAAGCUGCAGGCCUCUAAGGUGAAAGUCGAUACGCUGUCCGUCGAGGAAGCGUGUCGUCUGACCCCGCCCCAUUCCGCGCGAUCCAAGUUCGGAUACGGGGCUAAGGAGGUCCGUAGCUUG
#=GC SS_cons          :::::(((((-(((((((,,,<<<<--<<--<--<<<<<______>>>>>-->-->>---->>>>,,<<<<--<<<<<<<_________>>>->>>>-->>>>,,,,)))))))-))))):::
#=GC RF               aUuAAGcuccagGCgUCcAagGUcAAgGCuaGgcUcCUcuCcgUagAGgAAGCuUGCgacCUgACaCCcCCaCAcUCcGccaGaUCaAAgUguGGgUAuGGgGCaAAgGAcGUcCggagCcuu
//
