# STOCKHOLM 1.0
#=GF ID Tombus_3_III
#=GF AC RF00215
#=GF DE Tombus virus defective interfering (DI) RNA region 3
#=GF AU Daub J; 0000-0001-6022-563X
#=GF GA 35.0
#=GF NC 34.4
#=GF TC 35.1
#=GF SE PMID:12477830
#=GF SS Published; PMID:12477830
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 27.83 -Z 2958934 CM SEQDB
#=GF DR GO; 0019079; viral genome replication;
#=GF DR SO; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 12477830
#=GF RT An internally located RNA hairpin enhances replication of Tomato bushy
#=GF RT stunt virus RNAs.
#=GF RA Ray D, White KA
#=GF RL J Virol 2003;77:245-257.
#=GF CC This family represents region 3 of the defective interfering (DI) RNA
#=GF CC element of the Tombus viruses and is found in the 3' UTR. This family has
#=GF CC been found to enhance DI RNA accumulation by approximately 10-fold as well
#=GF CC as mediating viral replication [1].
#=GF WK Tombus_virus_defective_interfering_(DI)_RNA_region_3
#=GF SQ 28

AJ607402.1/4365-4434 AGCGAGUAAGACAGACUCUUCAGUCUGAUGUUACGGAGAUGAGUAGAACAAAGUGA--GGGACUAUGGGUUA
S43932.1/304-370     AGCUAGUAGGACAGACUCUUCAGUCUAGGUUGGUGGAAGCAGGAGAA--CACUGC---UUGACUAGCGGAGA
D00719.1/304-372     AGCUAGUAGGACAGACUCUUCAGUCUAGGUUGGUGGAAGCAGGAGAA--CA-CUGCUUGAGGGUACAGGUUU
X15511.1/4355-4423   AGCGAGUAGGACAGACUCUUCAGUCUAGGUUGGAGGAAGCAGGAGAA--CA-CUGCUUGAGGGUACAGGUUA
AY370535.1/1734-1802 AGCGAGUAAGACAGACUCUUCAGUCUGAUACUGCCGAAGCGAGUGAA--UA-CUGUUUGAGCAUGCAGGUUA
M59042.1/351-420     ACACCUGACUCCAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59041.1/395-461     AGAGA-AAAGACAGACUU--CAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
AY830918.1/4354-4422 AGCGAGUAAGACAGACUCUUCAGUCUGAGUUGGUGGAUGUGAGUGU---ACUUUGUUUGAGCAUACAGGUUA
AJ288944.1/511-579   AGCGAGUAAGACAGACUCUUCAGUCUGAUUGAGUGGAAGCAAGCACU--AACCUA-GAUAGCAUGUGGGUUG
AJ288915.1/511-579   AGCGAGUAAGACAGACUCUUCUGUCUGAUUGAGUGGAAGCAAGUACU--AACCUA-GAUUGCAUGUGGGUUA
AJ288918.1/511-579   AGCGAGUAAGACAGACUCUUCUGUCUGAUUGAGUGGAAGCAAGUACU--AACCUA-GAUAGCAUGUGGGUUA
AJ288934.1/511-579   AGCGAGUAAGACAGACUCUUCAGUCUGAUUGAGUGGAAGCAAGCACU--AACCUA-GAUAGCAUGUGGGUUA
AY579432.1/4388-4457 AGCGAGUAAGACAGACUCUUCUGCCUGAGUUCGCGGAUACAAGUGUG--AAUCUAACAACGCAUACAGGUUA
AF241533.1/266-335   AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGCGGAAACGAGUGUA--AAGCGGGCAUAGCAUACAGGUUA
AJ249740.1/4393-4462 AGCGAGUAAGACAGGCUCUUCAGUCUGAGUUCGCGGAAACGAGUGUG--AAUCUGACAACGUAUGCAGGUUA
Z68900.1/543-612     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUCGCGGAUAUGAGUGUG--AAUCUGACAACGCAUACAGGUUA
Z68899.1/543-611     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUCGCGGAAACGAGUGUA--AAUCUG-CAUAGCAUACAGGUUA
Z68897.1/540-609     AGCGAGUAAGACAGACUCUUCAGUCUGAGUGCGCGGAAACGAGUGUA--AAUCUGGCAACGCAUACAGGUUA
M59049.1/382-451     GGUGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGAAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
X62493.1/4413-4482   AGCGAGUAGGACAGACUCUUCAGUCUGAUUCUGUGGAAAUGAGAGUA--AUUCUGACAUAGCAUACAGGUUA
AF038044.1/352-421   GGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGCGGAAACGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59045.1/400-469     CGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
AJ288945.1/511-580   GGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
AJ288943.1/511-580   AGCGAGUAAGACAGACUCUUCUGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
U80935.1/4399-4468   AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGCGGAAACGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59043.1/392-461     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59046.1/399-468     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
X85215.3/4385-4454   AGCGAGUAAGACAGACUCUUCAGUCUGAGUUCGCUGAAACGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
#=GC SS_cons         ::::::::::<<<<<<<<________>>>>>>>>:::::::::::::..<<<<<<__________>>>>>>:
#=GC RF              AGCGAGUAAGaCagACUCUUCAGUCUGAGUuuGuGGAaAcGAGUGuA..aAcCuGgcAuAGcAUACaGgUuA
//
