# STOCKHOLM 1.0
#=GF ID Virus_CITE_4
#=GF AC RF02459
#=GF DE Necrovirus cap-independent translation element
#=GF AU Eberhardt R; 0000-0001-6152-1369
#=GF GA 40.0
#=GF NC 38.0
#=GF TC 47.5
#=GF SE Eberhardt R
#=GF SS Predicted; PMID:23192876
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 27.47 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory_region;
#=GF RN [1]
#=GF RM 23192876
#=GF RT Tombusvirus Y-shaped translational enhancer forms a complex with eIF4F and
#=GF RT can be functionally replaced by heterologous translational enhancers.
#=GF RA Nicholson BL, Zaslaver O, Mayberry LK, Browning KS, White KA
#=GF RL J Virol. 2013;87:1872-1883.
#=GF WK Cap-independent_translation_element
#=GF SQ 5

GQ221829.1/3489-3569         UGG---AGAUGGAUGCUGGAUCCUGGAAAACAGGUUU-AACGGGUAGGGGGUGGUGCCCCUACCGACGCAUCAC-UCCAGAUA---CCA
DQ083996.1/3504-3585         GCG---GUAAGCAAGACGGAUCCUGGGAAACAGGUUU-AACGGGCUGGGGGUGGUGCCCCGGCCGUCGCAUCACUUGCUGAUACAA---
#=GR DQ083996.1/3504-3585 PP ***...*******************************.************************************************...
FN543467.1/3454-3532         GAG---GUAUCGAUGCUGGAUCCUGGGAAACAGGCUU-GACAGGUUUG-GGUGGUUC-CAAACCGCUGCAUCAC-UCGAGAUA---CUC
#=GR FN543467.1/3454-3532 PP ***...*******************************.**********.69******.****************.********...***
AY616760.1/3484-3572         UGGGCGGUAAGCAAGAGGGAUCCUGGGAAACAGGCUUCGACGGGUUGGGGGUGGUGCCCCGGCCGACGCAUCACUUGCUGAUACAACCA
#=GR AY616760.1/3484-3572 PP **97778***************************76637**************************************************
D00942.1/3577-3660           UUG---ACGUACAAGCCGGAUCCUGGGAAACAGGUUU-AACGGGCUCACUGUGGUGG-UGGGCCGUCGAUACACUUGUAUGUGCCCCAA
#=GC SS_cons                 (((...(((((((((-((,,,<<<<_____>>>>,,,.,,,,<<<<<<__________>>>>>>,,))-----)))))))))----)))
#=GC RF                      ugG...acgugcAaGccGGAUCCUGGGAAACAGGuUU.aACGGGccgGggGUGGUgcCCcggCCGuCgcAuCACuUgcacguACaaCca
//
