# STOCKHOLM 1.0
#=GF ID rpfG
#=GF AC RF03023
#=GF DE rpfG RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 75.9
#=GF NC 75.4
#=GF TC 89.3
#=GF SE Weinberg Z
#=GF SS Published; PMID:28977401;
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 23.54 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 28977401
#=GF RT Detection of 224 candidate structured RNAs by comparative analysis of
#=GF RT specific subsets of intergenic regions.
#=GF RA Weinberg Z, Lunse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR,
#=GF RA Sherlock ME, Breaker RR
#=GF RL Nucleic Acids Res. 2017;45:10811-10823.
#=GF CC Xanthomonas (Gammaproteobacteria). Downstream gene
#=GF WK RpfG_RNA_motif
#=GF SQ 28

URS0000D68BFD_1321368/1-79 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCGGC-G----GUAU--CGCCGGGGAAGCUGGCCUAGGGGCCGGCGUGAU-GCUUC
URS0000D6A446_314565/1-84  GGCACAGAUACUGCAUAUGCUAGGGCGGAGCUUCGG-UCACGGU-GUGGCCGGAG-GAGUCGGUUCAGGGACCGACGUCGUCGCUUU
URS0000D66FBD_1182783/1-84 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCUCCGG-UCACGGU-AUGGCCGGAG-GAGUCGGUACAGGGACCGACGUCGUCGUUUU
URS0000D66FBD_340/1-84     GGCACAGAUACUGCAUAUGCUAGGGCGGAGCUCCGG-UCACGGU-AUGGCCGGAG-GAGUCGGUACAGGGACCGACGUCGUCGUUUU
URS0000D6AB6F_990315/1-84  GGCACAGAUACUGCAUAUGCUAGGGCGGAGCUCCGG-UCACGGUA-UGGCCGGAG-GAGUCGGUACAGGGACCGACGUCGUCGCUUU
URS0000D68CFB_925775/1-84  GGCACGGAUACUGCAUAUGCUAGGGCGGAGCUUCGG-GCAACGUCAUGUCCGGGG-GAGUCGACACAGCAGUCGACGUCA-CGCUUU
URS0000D679A4_190486/1-86  GGCACAGAUACUGCAUAUGCUAGGGCGGUUCCUCCGGACGGCGUAUCGUCGGAGG-UAGCCGGCGCGGGGGCCGGUGUCAUCGCUUU
URS0000D6C7FF_1131451/1-84 GGCACAGUUACUGCAUAUGCUAGGACAGAGCCGCGA-ACAGCGUACUGUUCGGGG--AGUCGGCACAGGGGGCGGCAUCACCGCUUU
URS0000D6AA0B_863365/1-84  GGCACAGAUACUGCAUAUGCUUGAGCGGAGCCCCGA-AUGGCGUAUCG-UCGGGG-GAGUCGGCAGUACCGUCGGCGUUAUCGCUUU
URS0000D6AA0B_925777/1-84  GGCACAGAUACUGCAUAUGCUUGAGCGGAGCCCCGA-AUGGCGUAUCG-UCGGGG-GAGUCGGCAGUACCGUCGGCGUUAUCGCUUU
URS0000D67987_1169848/1-84 GGCACAGAUACUGCAUAUGCUAGAGCGGAGCCCCGA-AUGGCGUAUCG-UCGGGG-GAGUCGGCCCGGCGGCCGGCGUCAUCGCUUU
URS0000D65ABA_559736/1-84  GGCACAGAUACUGCAUAUGCUAGGGCGGAGCUUCGA-ACAAGGUAUUGUUCGGGG-GAGUCGGCACAG-CGCCGGCGUUAUCGCUUU
URS0000D6C827_366649/1-86  GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGA-ACAGCGUAUCGUUUGGGGAUAGUCGGCGCAGGGGCCGGCGUCAUCGCUUU
URS0000D66FA8_1156940/1-86 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGA-ACAGCGUAUCGUUUGGGGAUAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D66FA8_1150615/1-86 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGA-ACAGCGUAUCGUUUGGGGAUAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D66FA8_1085630/1-86 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGA-ACAGCGUAUCGUUUGGGGAUAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D66FA8_1118965/1-86 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGA-ACAGCGUAUCGUUUGGGGAUAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D66FA8_1127439/1-86 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGA-ACAGCGUAUCGUUUGGGGAUAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D679B0_981368/1-85  GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCUCGA-ACAGCGUAUCGUUCGGGG-GAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D679B0_316273/1-85  GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCUCGA-ACAGCGUAUCGUUCGGGG-GAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D6A522_1189618/1-85 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGG-ACGGCGUAUCGUUCGGGG-GAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D6A522_1185662/1-85 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGG-ACGGCGUAUCGUUCGGGG-GAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D6A522_1185327/1-85 GGCACAGAUACUGCAUAUGCUAGGGCGGAGCCCCGG-ACGGCGUAUCGUUCGGGG-GAGUCGGCACAGGGGCCGGCGUCAUCGCUUU
URS0000D6BE60_1009853/1-85 GGCACACAUACUGCAUAUGCUAUGGCAGAGCCUCGA-ACAGCGUAUUGUUCGGGA-CAGUCGGCACAGACGCCGGCGUCAUCGCUUU
URS0000D669B2_1009854/1-85 GGCACACAUACUGCAUAUGCUAUGGCAGAGCCUCGA-ACAGCGUAUUGUUCGGGA-CAGUGGGCACAGGCGCCAGCGUCAUCGCUUU
URS0000D6AC03_12908/1-85   GGCACACUUACUGCAUAUGCUAGUGCAGAGCCUCGA-ACAGCGUAUUGUUCGGGA-GAGUCGGCACAGGCGCCGGCGUCAUCGCUUU
URS0000D6AC03_342109/1-85  GGCACACUUACUGCAUAUGCUAGUGCAGAGCCUCGA-ACAGCGUAUUGUUCGGGA-GAGUCGGCACAGGCGCCGGCGUCAUCGCUUU
URS0000D6C6ED_12908/1-85   GGCACACAUACUGCAUAUGCUAGGGCAGACCCUCGA-ACAGCGUAUUGUUCGGGA-GAGUCGGCACAGGUGCCGGCGUCAUCGCUUU
#=GC SS_cons               ::::::::::::::::::::::::::::::<<<<<<.<<<<____>>>>>>>>>>.::<<<<<<______>>>>>>:::::::::::
#=GC RF                    GGCACAGAUACUGCAUAUGCUAGGGCGGAGCccCGg.aCggcGUAccGucCGggG.gAGccGGCacAGggGCCggCGUcAUCGCUUU
//
