# STOCKHOLM 1.0
#=GF ID nrdJ
#=GF AC RF03034
#=GF DE nrdJ RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 40.3
#=GF NC 40.1
#=GF TC 41.0
#=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 26.64 -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 Streptomyces (Actinobacteria). Downstream gene
#=GF WK NrdJ_RNA_motif
#=GF SQ 73

URS0000D6A75E_1155718/1-84 ACCUGAGCCGG--GAC----G----AGAGCAGGG----C---GUC--CCGACUCCGGAAAGACAU-------ACAC-CGUGCC--AC-GGAAUUU-GUGG-GCACAUAUGGGCGUU
URS0000D6914C_1316445/1-84 UCCUGAACCGG--GGC----G----AGAGCAGGG----C---GCC--CCGGUUCCGGCAAGACAU-------ACAC-CGUGCC--AC-GGAAUUU-GUGU-GCACAUAUGGGCGUU
URS0000D6B644_1157640/1-84 ACCUGUGUCGG--GGC----G----AGAGCAGGG----C---GCC--CCGGUAUCAGAAAGACAU-------ACAC-CGUGCC--AC-GGAAUGC-GUGC-GCACAUAUGGGCGUU
URS0000D68650_1160718/1-84 ACCUGAACCGG--GGC----G----AGAGCAGGG----C---GUC--CCGGUGGCAGAAAGACAA-------ACAC-CGUGCC--AC-GGAAUGA-GUGC-GCACAUAUGGGCGUU
URS0000D6CF3C_996637/1-93  ACCUGUCACGC--GCACC--CCG--GCACCACA---CGG---UGC--GCGUGA-CCAGCAGACAC-ACCAC-ACACAAGUGCCA----GGAAGAA-ACGG-GCACUGAUGGGCGUU
URS0000D67291_1265868/1-84 ACCUGACCAGG--GCAAC--GU---GCAG--------AC----GC--CCUGGU-U-CC-AGACAG-A---ACACAC-CGUGCCA-CG-GGAAGAA-AGUGCGCACAUAUGGGCGUU
URS0000D67AA7_1203257/1-80 ACUUGGCCUGGACACG---------CAC--------------CGUGCCCGGGU-CAUC-AGACAG-G---C-ACA-----GCUCUCGGGGAAGAACCGGG-GCAUGUUGGGGCGUU
URS0000D69AC8_1203592/1-80 ACCUGGUCCGG--GUG----CG---CAG---------CG---UGC--CCGGAU-CACC-AGACAG-G---C-ACAG--AU-CUC-GG-GGAAGAACCGGG-GCAUGUUGGGGUGUU
URS0000D6A7AF_1286094/1-84 ACCUGUCGUGG--GUC----GUCC-GUAG------GGGC---G-C--CCGCGA-CAUCAAGACAC-------ACAC-CGUGCUG-CG-GGAAGAA-CGCG-GCACUUCAGGGCGUU
URS0000D68EAA_1352941/1-83 ACCCGUCACGA--GCGC---CC---CACGA-------GG---CGC--CCGUGG-CAAC-GGACAC-----A-UCAC-UGUGCCA-UG-GGAAGAA-CGUG-GCACUUCAGGGCGUU
URS0000D666CE_698760/1-83  ACCUGUUGCGG--ACA----GCA--UCGAG------UGC---UGU--CCGCAG-CGCA-AGAAAC-------ACAC-CGUGUCA-UG-GGAACAA-CGUG-ACACUUCUGGGCGUU
URS0000D6A475_12908/1-84   ACCCGUUGCGC--GCA----GCCG-CGAA------CGGC----GU--GCGCGA-CAAGCAGACAC-------ACAC-CGUGCC-ACG-GGAAGAA-CGAG-GCACUUCAGGGCGUU
URS0000D6CED2_1169154/1-81 ACCUGUUCCGG--GCGC---UG---UGAG--------CG-A-CGC--CCGGGA-CGAC-AGAAAC-------ACA--UGUGCCC-AG-GGAAGAC-AUGG-GCACUCCAGGGCGUU
URS0000D6CE15_12908/1-82   ACCUGUCACGG--GUG----CUG--CUCG-------CAG---UGC--UCACGA-CGAA-AGACGG-------AAAC-CGUGCCCUGG-GAAGCUAU--GG-GCACAUCAGGGCGUU
URS0000D6A57B_1306406/1-81 ACCUGUCACGG--GUG----CUG--CUCG-------CAG---CGC--UCACGA-CAAC-AGACGG-------AAAC-CGUGCCU-UG--GAAGAU-CUGG-GCACAUCAGGGUGUU
URS0000D6B4F1_1169158/1-85 AUGUGUCCCAG--GUG----CUGC-GUGGC-----GCGG---UGC--CCGGGA-CGUC-AGACAG-------AGAC-UGUGCCC-CG-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D6B4F1_1169155/1-85 AUGUGUCCCAG--GUG----CUGC-GUGGC-----GCGG---UGC--CCGGGA-CGUC-AGACAG-------AGAC-UGUGCCC-CG-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D66A85_457431/1-81  ACCUGUUCCCG-AGGC----CG---AGUG--------CG---GCCCACGG-GG-CAAC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D6732C_1303692/1-81 ACCUGUCCCCG-UGGC----CC---AGUG--------CG---GCCCGCGG-GA-CGAC-GGACAC-------ACAC-UGUGCCU--G-GGAAGAA-CUGG-GCACUUCAGGGCGUU
URS0000D67FDE_1155715/1-80 ACCUGUUCCCG--UGG----CCG--AGCG-------CGG--CCC---CGG-GG-CAAC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAA-CUGG-GCACUUCAGGGCGUU
URS0000D6C5AC_1085628/1-80 ACCUGUUCCCG--UGG----CCG--AGCG-------CGG--CCC---CGG-GG-CAAC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAA-CCGG-GCACUUCAGGGCGUU
URS0000D65C95_1172567/1-82 ACCUGUUCCCG--UGG----CCCG-AGUG------CGGC---CCA--CGG-GG-CAAC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D6B70D_1156841/1-81 ACCUGUUCCCG--CGG---CCCG--ACG--------UGG--CCCG--CGG-GG-CGAC-GGACAC-------ACAC-UGUGCCU--G-GGAAGAA-CUGG-GCACUUCAGGGCGUU
URS0000D67D23_1169156/1-82 AUGUGCUUCCG--GCU----GCCG-AGUG------CGGC---UUC--CGG-AG-CAUC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D67D23_1055352/1-82 AUGUGCUUCCG--GCU----GCCG-AGUG------CGGC---UUC--CGG-AG-CAUC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D6C4AC_455632/1-82  AUGUGCUUCCG--GCU----GCCG-AGUG------CGGC---UCC--CGG-AG-CAUC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D6C4AC_1609288/1-82 AUGUGCUUCCG--GCU----GCCG-AGUG------CGGC---UCC--CGG-AG-CAUC-GGACAC-------ACAU-UGUGCCU--G-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D66DC9_1134445/1-82 ACCUGCCGCGG--GUG----CCG--UGAA-------CGG---CGU--CCGCGG-CGGC-AGACAG-------AAAC-CGUGCUC-UG-GGAAGAU-UUGG-GCACAUAAGGGCGUU
URS0000D6B41F_680198/1-81  ---UGUCGUGA-ACGG----CU---GUCC--------AG---CCGGGUCGCGA-CACA-AGACAG-----A-ACAC-CGUGUCA-CG-GGAACAA-CGUG-ACACUUCAGGGCGUU
URS0000D65F9B_1054862/1-84 ACCUGUCGCGA-ACGG----CU---GUGC--------GG---CCGGGUCGCGA-CACA-AGACAG-----A-ACAC-CGUGUCA-CG-GGAACAA-CGCG-ACACUUCAGGGCGUU
URS0000D69538_698759/1-85  ACCUGUCGCGG-ACGGC---UG---UGCG--------AG---CCGGGUCGCGG-CACA-AGACAG-A---A-ACAC-CGUGCCA-CG--GAACAA-CGUG-GCACUUCAGGGCGUU
URS0000D66CEF_1312234/1-85 ACUUGUUGCGG-GGCCA---UG---AGCUG-------UG---GGCGCCCGCGG-CAUC-AGACAA-------ACAC-UCUGCCA-CG-GGAACAU-CGUG-GCAUUUUCGGGCGUU
URS0000D6B787_1306990/1-86 ACUUGUCGCGG-AGCCA---UG---AGCG--------UG-UGGGCUGCCGUGA-CACC-AGACAA-------ACAC-UCUGCCA-CG-GGAACAU-CGUG-GCAUUUCAGGGCGUU
URS0000D68A0C_1054860/1-82 ACCUGUCGUGA--GCA----CUG--AGCG-------CGG---UGU--UCACGG-CAAC-AGACAG-------AGAC-UGUGCCC-CG-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D6863D_1116232/1-87 ACCUGUUGCGG--GCGG---AAG--AGCG-------UUUGGGUGC--CCGCAA-CUUC-AGAAAU-----C-ACAC-UGUGUCA-CG-GGAACAA-CGUG-GCAUUUCUGGGCGUU
URS0000D6C4FA_700597/1-86  ACCUGUUGCGG--GUGG---CG---AUCCAG------CG--GUGC--CCGCGA-CACC-AGACAG-----A-ACCA-CGUGCCA-CG-GGGAACAUCGCG-GCACUUCAGGGCGUU
URS0000D6AD0B_1172181/1-86 ACCUGCUGUGG--GUGAU--AG---CGCG--------UG-GGUGC--CCACAG-CACA-AGACAG-----A-ACAU-CGUGUCA-CG-GGAACAAACGUG-GCAUUUUAGGGCGUU
URS0000D6BC3F_1078086/1-84 ACCUGUUGCGG-AGG-----GC---AGC---------GC-GAGUUGCCCGCAA-CACC-AGACAC-----A-ACAC-CGUGCC-ACG-GGAACAU-CGGG-GCACUUCAGGGCGUU
URS0000D6ABF4_1133850/1-85 ACCUGUUGCGG--GUGG---CA---GCUG--------AG-GGUGC--CCGCAG-CACA-CGACAG-----A-AACA-CGUGCCCAUA-GGAACAA-AUGG-GCACUUCAGGGCGUU
URS0000D68989_1214242/1-85 ACCUGUUGCGG--GCGGC--AG---CGUG--------AG-GGAGC--CCGCAG-CACC-AGACAG-----A-ACAC-CGUGUCA-CG-GGAACAU-CGUG-GCACUUCAGGGCGUU
URS0000D67C66_1352936/1-85 ACCUGUUGCGG--GUGG---CA---GCUG--------AG-GGUGC--CCGCAA-CUCA-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAAACGGG-GCACUUCAGGGCGUU
URS0000D66E5F_566461/1-83  ACCUGUUGCGG--GUGGA--CC---AGUG--------GG---CGC--CCGCAG-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GAAACAA-CGGG-GCACUUCAGGGCGUU
URS0000D67BC3_467200/1-84  ACCUGUUGCGG--GCAGG--CG---AGUG--------GG---CAC--CCGCAG-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAAUCGGG-GCACUUCAGGGCGUU
URS0000D66214_1157639/1-83 ACCUGUUGCGG--GCAGG--CG---AGUG--------GG---UGC--CCGCAG-CAUC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAU-CGGG-GCACUUCAGGGCGUU
URS0000D682FB_1284664/1-84 ACCUGUUGCGG--GCAGG--CG---AGUG--------GG---UGC--CCGCAG-CAUC-AGACAG-----A-ACAC-CGUGCCCACG-GGAACAU-CGGG-GCACUUCAGGGCGUU
URS0000D66461_463191/1-85  ACCUGUUGCGG--GCGG---UA---GCGAG-------UG-GGUGC--CCGCAA-UACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAA-CGGG-GCACUUCAGGGCGUU
URS0000D6AF85_1172183/1-84 ACCUGUUGCGG--GCGG---UA---GCGAG-------UG-GGCGC--CCGCAA--ACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAA-CGGG-GCACUUCAGGGCGUU
URS0000D6593A_1172180/1-85 ACCUGUUGCGG--GCGG---UA---GCGAG-------UG-GGUGC--CCGCAG-CAUC-AGACAA-----A-ACAC-CGUGUCA-CG-GGAACAU-CGUG-GCACUUCAGGGCGUU
URS0000D67D02_457428/1-85  ACCUGUUGCGG--GCGGA--G----CGAG---------C-GAUGC--CCGCAA-CACC-AGACAG-----A-ACAC-CGUGCCCACG-GGAACAAUCGGG-GCACUUCAGGGCGUU
URS0000D67D02_100226/1-85  ACCUGUUGCGG--GCGGA--G----CGAG---------C-GAUGC--CCGCAA-CACC-AGACAG-----A-ACAC-CGUGCCCACG-GGAACAAUCGGG-GCACUUCAGGGCGUU
URS0000D68C7A_1120227/1-85 ACCUGUUGCGG--GCGCG--G----CGAG---------A-GAUGC--CCGCAA-CACC-AGACAG-----A-ACAC-CGUGCCCACG-GGAACAAUCGGG-GCACUUCAGGGCGUU
URS0000D6810A_1214101/1-84 ACCUGUUGCGG--GCGGC--AG---UGAG---------A-GAUGC--CCGCAA-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAU-CGGG-GCACUUCAGGGCGUU
URS0000D6907F_1073567/1-84 ACCUGUUGCGG--GCGG---CG---UGAG--------CG-A-UGC--CCGCAA-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAAACGGG-GCACUUCAGGGCGUU
URS0000D65B31_591159/1-84  ACCUGUUGCGG--GCUG---UG---UGAG--------UG-GAUGC--CCGCAA-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAA-CGGG-GCACUUCAGGGCGUU
URS0000D68712_1283301/1-84 ACCUGUUGCGG--GCGA---GG---UGAG--------UG-GGUGC--CCGCAA-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAA-CGGG-GCACUUCAGGGCGUU
URS0000D6C955_1079986/1-84 ACCUGCUGCGG--GCGA---UG---UGAG--------UG-GGUGC--CCGCAG-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGAACAA-CGGG-GCACUUCAGGGCGUU
URS0000D664EB_1160705/1-86 ACCUGUUGCGG--GCGGCGAUC---AGA---------GG--GUGC--CCGCAG-CACC-AGACAG-----A-ACAC-CGUGCC-ACG-GGGAACAUCGGG-GCACUUCAGGGCGUU
URS0000D66D7C_1156844/1-82 ACCUGUUGCGG--GCGG---CG---AGAG--------CG-G-CGG--CCGCGA-CACA-AGACAC-------ACAC-CGUGCCA-CG-GGAAGAA-CGCG-GCACUUUUGGGCGUU
URS0000D68EB2_1157638/1-85 ACG-GCUGCGG--GCGG---CG---GCGACACA----CG---UGC--CCGCGG-CACC-GGACAG-----A-ACAC-CGUGUCU-CG-G-AACAUUCGGG-GCACUUCUGGGCGUU
URS0000D66ACC_645465/1-83  ACG-GCUGCGG--GCG----GCAG-GGAA------CAGG---UGC--CCGCAG-CACC-AGACAG-----A-ACAC-CGUGUCC-CG-G-AACAU-CGGG-GCACUUCAGGGCGUU
URS0000D68E4B_1155714/1-82 ACCUGUCGCGG--GUGG-CGCC----GAA--------GG---UGC--CCGCGA-CGCA-AGACAG-----A-ACAC--GUGUCC-UG-GGAACAU-CGGG-GCACUUCAGGGCGUU
URS0000D6C46F_1156843/1-88 -CUUGCUCCGGGCGAC----GUAU-GACGA-----AUGC---GGCGGCCGAAG-CAUC-AGACAC-------ACAC-UGUGCCC-GG-GGAAGUU-CUCG-GCACUUCAGGGCGUU
URS0000D6C46F_1157633/1-88 -CUUGCUCCGGGCGAC----GUAU-GACGA-----AUGC---GGCGGCCGAAG-CAUC-AGACAC-------ACAC-UGUGCCC-GG-GGAAGUU-CUCG-GCACUUCAGGGCGUU
URS0000D6B712_1157635/1-88 -CUUGUUCCGG--GCGA---CGUAUGACGA----AUACG----GCGGCCGAAG-CAUC-AGACAC-------ACAC-UGUGCCC-GG-GGAAGUU-CUCG-GCACUUCAGGGCGUU
URS0000D670EA_457429/1-82  ACCUGCUCGUG--GGC----GCUG-UGCG------UGGC---GU---CA-GAG-CAAC-AGACAC-------AAAC-CGUGCCC-CG-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D6D0D3_862751/1-83  ACCUGCUCCGC--GGC----GCUG-UGCG------UGGC---GCC--GCG-AG-CAUC-AGACAC-------ACAC-UGUGCCC-UG-GGAAGAA-CUGG-GCACUUCAGGGCGUU
URS0000D6AFEE_1265601/1-83 ACCUGUUCCGG--GAC----GCUG-UGCG------CGGC---GU---CCGGAA-CAUC-AGACAC-------ACAC-UGUGCCC-UG-GGAAGAA-CUGG-GCACUUCAGGGCGUU
URS0000D69B03_457427/1-80  ACCUGCCCGGG--GCG---------CAUCG------------CGCC-UCCGGG-UGAA-AGACAAGA---G-ACAC-CGUGCCC--G-GGAAGAA-AUGG-GCACAUCAGGGCGUU
URS0000D6CF24_1343740/1-80 ACCCGCCCGGG--GCG---------CUUGU------------CGCG-UCCGGG-UGAA-AGACAG-A---C-ACAC-CGUGCCC-GG-GGAAGAA-AUGG-GCACAUCAGGGCGUU
URS0000D6BD90_653045/1-77  ACCUACCCGGG--GCG---------CUUGC------------CGCA-UCCGGG-UGAA-AGACAG-------AUA--CGUGCCU-GG-GGAAGAA-AUGG-GCACAUCAGGGCGUU
URS0000D690BF_1223523/1-78 ACCUGCCCGGU--GCGC--------CCCCG------------CGCA-CCCGGG-CGAA-CGACAC-------ACAU-CGCGC-C-AU-GGAAGAA-AUGU-GCGCACAAGGGCGUU
URS0000D6CA1F_1114943/1-77 ACCGACCGUGA--GCG---------CUCGG------------CGCGCACGGUA-UCCA-AGACAG---------GC-AGUGCC-ACG-GGAAGAU-CUGG-GCACUUCAGGGCGUU
URS0000D689A3_443255/1-80  AUCGUUCAUGG--ACG----CU---CGGG--------GG---CGU--CCGUGA-CACC---ACAG-A---C-AGAC-CGUGCCC-UG-GGAAGAU-CUGG-GCACUUCAGGGCGUU
#=GC SS_cons               :::<<<<<<<<..<<<....<<...____........>>...>>>..>>>>>>.>>::.::::::.......::::.:<<<<<<.<<._______.>>>>.>>>>:::::::::::
#=GC RF                    ACCuGccgcGg..Gcg....cc...agaG........gg...cgC..cCgcgg.Caac.AGACAg.......ACAC.cGUGCCc.cg.GGAAgAa.cggG.GCACUUcAGGGCGUU
//
