# STOCKHOLM 1.0
#=GF ID Flavi_ISFV_repeat_Ra
#=GF AC RF03544
#=GF DE Insect-Specific Flavivirus 3' UTR repeats Ra
#=GF AU Wolfinger MT; 0000-0003-0925-5205
#=GF GA 41.0
#=GF NC 39.3
#=GF TC 46.8
#=GF SE Lamkiewicz K
#=GF SS Predicted; LocARNA 2.0.0RC8
#=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 CL CL00131
#=GF DR SO; 0000837; UTR_region;
#=GF RN [1]
#=GF RM 17070886
#=GF RT Genetic characterization of a new insect flavivirus isolated from Culex
#=GF RT pipiens mosquito in Japan.
#=GF RA Hoshino K, Isawa H, Tsuda Y, Yano K, Sasaki T, Yuda M, Takasaki T,
#=GF RA Kobayashi M, Sawabe K
#=GF RL Virology. 2007;359:405-414.
#=GF RN [2]
#=GF RM 30909641
#=GF RT Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and
#=GF RT No-Known-Vector Flaviviruses.
#=GF RA Ochsenreiter R, Hofacker IL, Wolfinger MT
#=GF RL Viruses. 2019; [Epub ahead of print]
#=GF CC 3' UTR in insect specific flavivirus families present three to four
#=GF CC repeats of conserved element Ra [1,2].
#=GF WK Flavivirus_3'_UTR
#=GF SQ 30

AB262759.2/10477-10526 GCCAUCGCAAGGGAGGA---------------UUUUCCUCGGGUACUGACCAUACCCCGACCCCA
FJ644291.1/10619-10672 GCCACCGCAAGGGAGAGGGA-----------UCCCCUCUCGGGUUUGGACGACACCCCGGCCCCA
AB981186.1/10618-10669 ACCACCGCAAGGGAGGGGAU-----------U--CCCCUCGGGUGUGGACGACACCCCGGCCCCA
AB981186.1/10486-10549 GCCCGCGCAAGGAAAGACGUGGAGCAGUCCGC-GAUCUUUGGGAGUUGACGACUCUCCGCCCCCA
FJ644291.1/10489-10550 GCCCGCGCAAGGAAGGACACGUAA-AUCACGU--GUUCUUGGGAGUUGACGACUCUCCGCCCCCA
MH827524.1/10513-10574 GCCCGCGCAAGGAAGGACACGUGA-AUGACGU--UUCCUUGGGAGUUGACGACUCUCCGCCCCCA
KC464457.1/10488-10551 GCCCGCGCAAGGAAGGAUGCGAUG-AAAACGCUUGUCCUUGGGAGUUGACGACUCUCCGCCCCCA
AB981186.1/10338-10399 GCCCCCGCAAGGAGGAACGUGU-CACUGGCAU--GUUCCUGGGAGUUAACGGCUCUCCGGCCCCA
FJ644291.1/10343-10402 GCCCCCGCAAGGAGGGGUGUGU-GUUU--CAC--GCCCCUGGGAGUUAACGAUUCUCCGGCCCCA
MH827524.1/10367-10426 GCCCCCGCAAGGAGGGACGUGC-UUUU--CAC--GUCUCUGGGAGUUGACGACUCUCCGGCCCCA
KC464457.1/10342-10401 GCCCCCGCAAGGAGGGACGUGU-GCAU--CAC--GUUUCUGGGAGUUAACGGCUCUCCGGCCCCA
HE574573.1/10405-10461 CCACCCGCAAGGGGAGGGUU------UUCUAA--CUCUCCGGGUGUUGACGACACCCCGGCCCCA
KX652375.1/10551-10607 CCACCCGCAAGGGGGGAGUU------UUCUAA--CUCCCCGGGUGUUGACGACACCCCGGCCGCA
MF582365.1/10405-10461 CCACCCGCAAGGGGGGAGAU------UUCCAA--CUCCCCGGGUGUUGACGACACCCCGGCCCCA
MF582366.1/10276-10333 GCCCACGCUAGGGGGUAGAG------UAGACUC-AUCUCCGGGUGUUGACGACACCCCGACCCCA
MF582365.1/10276-10333 GCCCACGCAAGGGGAGAGAA------GAUUUUC-GCCUCCGGGUGUUGACGACACCCCGACCCCA
KX652377.1/10423-10479 GCCCACGCAAGGGGAGGCAU--------CAUAUUGCCUCCGGGUGCUGACGACACCCCGUCCCCA
HE574573.1/10278-10334 GCCCACGCAAGGGGAGGCAU--------CAUUUCGCCUCCGGGUGCUGACGACACCCCGCCCCAG
HE574574.1/10278-10334 GUCCACGCAAUGGGAGGCAU--------CAUUUCGCCUCCGGGUGCUGACUACUCCCCGUCCCCG
EU879060.1/10245-10299 AACCCCGCAAGGAAGGACUAGG----------CUGUCCUUGGGUGCUAACGACACUCCGGCCCCA
AB701766.1/10245-10299 AACCCCGUAAGGAAGGACAAGG----------CUGUCCUUGAGUGCCAACGACGCUCCGGCCCCA
AB262759.2/10245-10299 AACCCCGUAAGGAAGGACAAGG----------CUGUCCUUGAGUACUAACGACACUCCGGCCCCA
AB262759.2/10364-10418 ACGCGCGCAAGGAAGGACAUGG----------CUGUCCUUGGGUACGAACGACACCCCGCCCCCA
KY349933.1/10362-10416 AAGCGCGCAAGGAAGGACAUGG----------CUGUCCUUGGGUACUAACGACACCCCGCNNNNN
HQ678513.1/10368-10422 AUGCGCGCAAGGAAGGACAUGG----------CUGUCCUUGGGUACUAACUACACCCCGCCCCCA
AB262759.2/10597-10647 GCUCCCGUAAGGAAAGCG--------------CAAGCUUUGAGCAUUGACAACGCUCCGGCCCCA
AB981186.1/10239-10297 GGCAGCGCAAGGAAGGUGGG------CUGGAUGCCGCCUUAGGUGGUGACGACACCUCGCCCCCA
FJ644291.1/10244-10302 UUCAGCGCAAGGAAGGGAAG------CUUGAGGCUACCUUAGGUGGUGACGACACCUCGCCCCCA
KC464457.1/10243-10301 UUCAGCGCAAGGAAGGAAAG------CUGGACGCUACCUUAGGUGGUGACGACACCUCGCCCCCA
HE574573.1/10177-10235 GCUAGCGCAAGGAAGGAAAG------UUGCAGACUACCUUGGGUGUUGACGACACUCCGCCCCCA
#=GC SS_cons           ::::(((,,,,,<<<<<<__......_.______>>>>>><<<<<<_____>>>>>>))):::::
#=GC RF                GCCCgCGCAAGGAaGGacAu......u.ccaucuguCCuUGGGuGuUGACGaCaCCCCGcCCCCA
//
