# STOCKHOLM 1.0
#=GF ID Flavi_ISFV_repeat_Ra_Rb
#=GF AC RF03542
#=GF DE Insect-Specific Flavivirus 3' UTR repeats Ra and Rb elements
#=GF AU Wolfinger MT; 0000-0003-0925-5205
#=GF GA 50.0
#=GF NC 41.1
#=GF TC 67.4
#=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 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 RN [2]
#=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 CC 3' UTRs in insect specific flavivirus families present three to four
#=GF CC repeats of conserved element Ra and Rb [1,2].
#=GF WK Flavivirus_3'_UTR
#=GF SQ 12

NC_008604.2/10482-10571 CGCAAGGGAGGAUUU--------------UCCUCGGGUACUGACCAU-ACCCCGACCCCAGUCCGAUA-GG--UCAU-G---GAA-UGA----CCCC---AUGGUGCUGAGAGGGC-AUCC-
NC_012671.1/10494-10595 CGCAAGGAAGGACACGUAAAUCACGU--GUUCUUGGGAGUUGACGAC-UCUCCGCCCCCAGUCCC-CA-GG--UCAG-G---GUA-UGA----CUCC---GUGGUGUUGAAAGGAC-ACUAA
NC_021069.1/10493-10596 CGCAAGGAAGGAUGCGAUGAAAACGCUUGUCCUUGGGAGUUGACGAC-UCUCCGCCCCCAGUCCC-CA-GG--UCAG-G---GUA-UGA----CCCC---GUGGUGUUGAAAGGAC-ACUAA
NC_012671.1/10348-10447 CGCAAGGAGGGGUGUGUG--UUUCAC--GCCCCUGGGAGUUAACGAU-UCUCCGGCCCCAGUUCC-UA-GG--UCCA-G---G----GA-GGGCCCC---GUGGCGCUGAAAGGGC-GCUGA
NC_021069.1/10347-10446 CGCAAGGAGGGACGUGUGCAU--CAC--GUUUCUGGGAGUUAACGGC-UCUCCGGCCCCAGUUCC-UA-GG--UCCA-G---GUA-GGA----UCCC---GUGGCGCUGUGAGGGC-GCUAA
NC_008604.2/10369-10463 CGCAAGGAAGGA--CAUGG---CUG----UCCUUGGGUACGAACGAC-ACCCCGCCCCCAGUUCUCAA-GG--UUAGAG---UUA-UAA----CCUC---AGGGUGUUGGAA-GAC-AUCC-
NC_012671.1/10249-10347 CGCAAGGAAGGGAAGCUUGA--GGCUA---CCUUAGGUGGUGACGAC-ACCUCGCCCCCAGUCUCCCG-GG--UUGGGGAUAAUA-CAA----CCUC---GUUGGGCU---ACUGC-CCC--
NC_021069.1/10248-10346 CGCAAGGAAGGAAAGCUGGA--CGCUA---CCUUAGGUGGUGACGAC-ACCUCGCCCCCAGUCUCCCA-GG--UUGGGGAUCGUA-CAA----CUUC---GUUGGGCU---AUUGC-CCC--
NC_021069.1/10625-10718 CGCAAGGGAGAG--GGAU----UCC----CUCUCGGGUGUGGACGAC-ACCCCGGCCCCAGUCCCCUA-GG--UCAUGGGAAAAACUGA----CCCCGAAGUGCUGC-------AA-GGG--
NC_012671.1/10624-10717 CGCAAGGGAGAG--GGAU----CCC----CUCUCGGGUUUGGAC-GACACCCCGGCCCCAGUCCCCCA-GG--UCAUGGGAAAAACUGA----CCCCGAAGUGCUGC-------AA-GGG--
NC_008604.2/10250-10344 CGUAAGGAAGGA--CAAGG---CUG----UCCUUGAGUACUAACGAC-ACUCCGGCCCCAG--------UU--CCCAG---AGCCAGGGUUUUAGCUCCACGGUGCUGGA----AGUCACCC
NC_008604.2/10602-10692 CGUAAGGAAAGCGCAA-------------GCUUUGAGCAUUGACAAC-GCUCCGGCCCCAGUCCCCCAGGUUAUGGGAGAAUAACCCCG----AC--------GUGCUGGAAGGGC-----A
#=GC SS_cons            :((--((<<<<<--<<___..._>>....>>>>><<<<<<_____>>.>>>>,,,,))--))::::::.<<..<<<___..____.>>>....>>::...:<<<<<<<_____>>>.>>>>:
#=GC RF                 CgCAAGGaaGGguacgugg...ucg....cCCuuGgGuguUgACgac.aCcCCGgCCCCAGucCccuA.gg..ucgggG..aguA.cga....cccC...ggggcgccGaaAgggc.gccca
//
