# STOCKHOLM 1.0
#=GF ID RAGATH-21
#=GF AC RF03097
#=GF DE RAGATH-21 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 70.3
#=GF NC 60.4
#=GF TC 76.6
#=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 27.46 -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 Clostridiales (Firmicutes). Nearby to self-cleaving ribozyme genes
#=GF WK RAGATH_RNA_motifs
#=GF SQ 38

URS0000D69B07_12908/1-108 UGCGCAUGCCCUUAAAAGAAACAAGAGGA---------UUUCAUGUGUAUAUAUUCCUUCCUAAAAAUUGUUCUU---------UUCUCUUGGAGGAU--AAAGUGGAUGCAAUGUCCAGCAUGCGCA
URS0000D69846_12908/1-72  UGUGUGCGCCCUUAAAAGAAAUCCCC------------AGCUA--------------------------------------------GGGGAGAGGUUGAAAAGCGGAUGCAAUUUCCGGCGCACACU
URS0000D69D5D_12908/1-76  UGAAUAUGUCCUUAAGAGAAACAGAUUC----------GAGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUAUUCA
URS0000D658EA_12908/1-76  UGAAUAUGUCCUUAAUAGAAACAGAUUC----------GAGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGACAUAUUCA
URS0000D6C575_12908/1-76  UGAAUAUGUCCUUAAUAGAAACAGAUUU----------GAGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGGUGCAAUUUCCGACAUAUUCA
URS0000D6C474_12908/1-76  UGAAUAUGUCCUUAAUAGAAACAGAUUU----------GAGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGGUGCAAUUUCCGGCAUAUUCA
URS0000D6CA19_12908/1-76  UGAAUAUGUCCUUAAUAGAAACAGAUUU----------GAGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUAUUCA
URS0000D68C80_12908/1-76  UGAAUAUGUCCUUAAUAGAAACAGAUUU----------GAGCG------------------------------------------GAAUCUGGAGGUUGGAAAGCGGAUGCAAUUUCCGGCAUAUUCA
URS0000D68F1C_12908/1-85  UGAAUAUGCCCUUAAGAGAAACAGAUGAAGC-------AGAUCUGA------------------------------------GCGGAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUAUUCA
URS0000D69AC1_12908/1-85  CGAAUAUGCCCUUAAGAGAAACAGAUGAAGC-------AGAUUUGA------------------------------------GCGGAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGACAUAUUCA
URS0000D69CBA_12908/1-85  CGAAUAUGCCCUUAAGAGAAACAGAUGAAGC-------AGAUUUGA------------------------------------GCGGAAUCUGGAGGUUGAAAAGCGGGUGCAAUUUCCGGCAUAUUCA
URS0000D6A484_12908/1-85  CGAAUAUGCCCUUAAGAGAAACAGAUGAAGC-------AGAUUUGA------------------------------------GCGGAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUAUUCA
URS0000D68F2F_12908/1-76  GGUGCGUGUCCUUAAUAGAAACAGGUUU----------GGACG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGACGCAAUUUCCGACACGUACC
URS0000D6BEB4_12908/1-77  GAUGCGUGUCCUUAAUAGAAACAGGUUC----------GGGGUG-----------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGACACGUAUC
URS0000D67C3B_12908/1-76  GAUGCGUGUCCUUAACAGAAACAGGUUC----------GGGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCACGUAUC
URS0000D68955_12908/1-76  GGUACGUGUCCUUAACAGAAACAGGUUC----------GGGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGACACGUAUC
URS0000D67168_12908/1-76  GGCGCGUGUCCUUAACAGAAACAGGUUC----------GGGCG------------------------------------------GAACCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGACACGUACC
URS0000D6C258_12908/1-76  GGUGCGUGUCCUUAACAGAAACAGAUUC----------GGGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCACGUGCC
URS0000D6AA91_12908/1-76  GGUGCGUGUCCUUAACAGAAACAGAUUC----------GGGCG------------------------------------------GAAUCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGACACGUACC
URS0000D691A3_12908/1-86  GAUGCGUGUCCUUAAUAGAAAAUGCA-------GUGUUUAGCU--------------------------------AACAC---AAGACGCAUGAGGUUGAAAAGCGGAUGCAAUUUCCGGCACGUAUC
URS0000D66959_12908/1-86  GGUGCGUGUCCUUAAUAGAAAAUGCA-------GUGUUUAUCC--------------------------------AACAC---AAGAAGCAUGAGGUUGAAAAGCGGACGCAAUUUCCGACACGCGCC
URS0000D6BA60_12908/1-89  GGUGCGUGUCCUUAAUAGAAAAUGCA------GUGAC-CGGAUU--------------------------------GUCACAUAAGAAGCAUGAGGUUGAAAAGCGGAUGCAAUUUCCGACGCGUACC
URS0000D6C7F9_12908/1-89  GGUGCGUGUCCUUAAUAGAAAAUGCA------GUGGC-CGGAUU--------------------------------GCCACAUAAGAAGCAUGAGGUUGAAAAGCGGAUGCAAUUUCCGACGCGUACC
URS0000D68CAA_12908/1-86  GGUACGUGUCCUUAAUAUAAAAUGCA------GUGUU-UAGCU---------------------------------AACAC--AAGAAGCAUGAGGUUGAAAAGCGGAUGCAAUUUCCGACACGUACC
URS0000D6BB64_12908/1-93  CGCGCACGUCCUUAAAAGAAAGAGAAUU-----GCAACAAAUUGCAAUCA-------------------------GUUGC-----AAAUCUUGAGGUUGAAAAGCGGAUGCAAUUUCCGGCGUGUGCA
URS0000D6CB52_12908/1-70  CGCGCACGUCCUUAAUAUAAACAGG-------------UCAUU---------------------------------------------CCUGGAGGUUGAAAAGCGGAUGAAAUUUCCGGCGUGCGCU
URS0000D66970_12908/1-70  CGCGCACGUCCUUAAUAUAAACAGG-------------CCAUU---------------------------------------------CCUGGAGGUUGAAAAGCGGAUGAAAUUUCCGGCGUGCGCU
URS0000D6A24F_12908/1-87  AGCACGCGUCCUUAAAAGAAACCGGCGUAC--------AUCCUCCAAAAG---------------------------------GUGCGCCGGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCGUGUGCA
URS0000D6850B_476272/1-69 AGCACACGUCCUUAAAAGAAACGGC-------------UCCG----------------------------------------------GCCGGAGGUUGAAAAGCGGGCGCAAUUCCCGACGUGUGCA
URS0000D6850B_12908/1-69  AGCACACGUCCUUAAAAGAAACGGC-------------UCCG----------------------------------------------GCCGGAGGUUGAAAAGCGGGCGCAAUUCCCGACGUGUGCA
URS0000D66EC4_12908/1-69  AGCACACGUCCUUAAAAGAAACGGC-------------UCCG----------------------------------------------GCCGGAGGUUGAAAAGCGGGCGCAAUUCCCGGCGUGUGCA
URS0000D68220_12908/1-70  AGCACACGUCCUUAAUAGAAACGGC-------------UUUAU---------------------------------------------GCCGGAGGUUGAAAAGCGGGUGCAAUUUCCGGCGUGUGCA
URS0000D691E7_12908/1-70  AGCACACGUCCUUAAUAGAAACGGC-------------UUUAU---------------------------------------------GCCGGAGGUUGAAAAGCGGGGGCAAUUUCCGGCGUGUGCA
URS0000D6C5DC_12908/1-87  UGCACAUGUCCUUAAUAGAAACGGGUC-CUAAUG----CAUAG------------------------------------CAUAAACGGCCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUGUGCG
URS0000D6888E_999406/1-87 AGCACAUGUCCUUAAAAGAAACAGGUUC-UAGCGC---AUA-------------------------------------GCGUGAACAGCCUGGAGGUUGAAAAGCGGAUGCGAUUUCCGGCAUGUGCG
URS0000D66081_997895/1-87 AGCACAUGUCCUUAAAAGAAACAGGUUC-UAGCGC---AUA-------------------------------------GCGUGAACAGCCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUGUGCA
URS0000D68444_999410/1-87 AGCACAUGUCCUUAAAAGAAACAGGUUC-UAGCGC---AUA-------------------------------------GCGUGAACAGCCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUGUGCG
URS0000D68444_12908/1-87  AGCACAUGUCCUUAAAAGAAACAGGUUC-UAGCGC---AUA-------------------------------------GCGUGAACAGCCUGGAGGUUGAAAAGCGGAUGCAAUUUCCGGCAUGUGCG
#=GC SS_cons              ((((((((((,,,,,,,,,,,<<<<<<<.........._____..........................................>>>>>>>,,,<<<____>>><<<_______>>>))))))))))
#=GC RF                   uGcgcguGcCCUUAAuAGAAAcgGguuc..........uaauu..........................................gaacCcgGAGGuUGAAAAgCGGaUGCAAUUuCCGgCacgcgCa
//
