# STOCKHOLM 1.0
#=GF ID RT-12
#=GF AC RF03016
#=GF DE RT-12 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 44.2
#=GF NC 43.8
#=GF TC 49.3
#=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 28.51 -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 Proteobacteria. Nearby to self-splicing intron genes
#=GF WK RT_RNA_motifs
#=GF SQ 42

URS0000D69403_391774/1-139  GAACUGUGCAGGAUUACAAGCGCAUGGCCUUGC-----AUCU-------------GCAAGGUGUUGUGGCUGAAAGGCACCC---UUCCCGAGGGUCCGGUCAAUGCCGAAAGAGCGAUUA-UGGGAC-GAUCCGA-AUCCUAU-GCUCUUUCGGUU-UUGCCAA
URS0000D6B7B4_1073969/1-121 UAACACUG-GCGGCUGC--GUAUC--------------ACUCUAG-------------------GGUACGUGAUA---GUGCGAUAUAAGAAGCACUGGUACAUGCCGGCAGGGACAGUUA-AGAGAU-GGCCGCA-GUCUCGU-GUCCCUGCCGGU-UUGGCUA
URS0000D6CABB_12908/1-127   UAACACAC-GCGGUUC---GCCGCCAGGC---------UAAUG----------------GCCUGCUGGCAAGAAG---GUGG--AUUAAAUGCCACUCAGGUA-AGCCGGAAGGGGACACAAUGAGAU-GACCGCA-GUCUCGUGCCCCUUCCGGUU-UGGCUAG
URS0000D68CE8_1119528/1-118 UAACACGC-GUGGCGAC--GCUGUGC------------CUUGU-------------------GCAUCGCAAGAUA---GUGA---UGAGUUAUCACUUGGUUA-AGCCGGGGAGGGUGUA--AGAGAU-UGCCACG-GUCUCAU-CCCUCUCCGGUU-UUGCUAU
URS0000D6CC80_12908/1-116   UAACACGC-GUGGCUAG--GUGGUAC------------UUUU--------------------GUAUCGCCGGAUGG--UGAU-----GAGUAGUCAUCGGUUA-AGCCGGAGGGGGUGCU--ACAGAU-UGCCACG-GUCUUAU-CUCCCUCCGGUU-UUGCUAA
URS0000D674C6_589865/1-109  UAACAGUC-GCGGCGC---GUACC--------------UCCG----------------------AGUAC-GGAAGG--GGUU------AGUAAACCUUUGGCUAAGCCGGAAGGGAUAUU---UGGAU-GGCCGCA-GUCCUAC-UCCCUUCCGGUU-UUGCAGA
URS0000D6B8D8_12908/1-119   UAACAUAC-GCGGCCAAA-GCACGGC------------UUUAC-------------------GUCGGGCUUGAUA---GUGU-----GAGGAACAUUUUGGUACAUCCGGGAGGGUGAUCA-ACGGAU-CGCCGCC-AACCAAC-ACCCUCUCGGUU-UGCUAGC
URS0000D688F8_1127483/1-118 UAACAUUAAGCGGCCAAA-GCCCAU-------------GCAA---------------------AUGGGUGAGAUG---AUGC-----GAAGAGCGUUUGUGUAUAUCCGGGGGAGUGGCCUAUAGGA-AUGCCGCCA-ACCUUC-AUUCCCCCGGUU-UGCUAGG
URS0000D6CE00_1158293/1-111 UAACAAAC-GCGGCCAG--GCCC---------------CUAACA---------------------GGGUGAAAUG---GUAA-----UAAGAUUACUC-GGUUUAUCCGGAAGGGCGGUUC-GUAGAU-UGCCGCC-AUCUUC--GCUCUUCCGGUU-UGCUAAG
URS0000D6AE47_690598/1-113  UAGCAAUC-GCGGUGAG--GCCGG--------------GUAA----------------------CCGGUUAGAUG---GUGU-----GAAGAACAUUUGGGUUUAUCCGACCGAGCGGCUG-AAGGAU-UGCCGCC-AUCCUAU-GCUCGGUCGGUU-GGCUCGA
URS0000D6AE47_1194406/1-113 UAGCAAUC-GCGGUGAG--GCCGG--------------GUAA----------------------CCGGUUAGAUG---GUGU-----GAAGAACAUUUGGGUUUAUCCGACCGAGCGGCUG-AAGGAU-UGCCGCC-AUCCUAU-GCUCGGUCGGUU-GGCUCGA
URS0000D6AE47_1194423/1-113 UAGCAAUC-GCGGUGAG--GCCGG--------------GUAA----------------------CCGGUUAGAUG---GUGU-----GAAGAACAUUUGGGUUUAUCCGACCGAGCGGCUG-AAGGAU-UGCCGCC-AUCCUAU-GCUCGGUCGGUU-GGCUCGA
URS0000D694E0_1200345/1-124 UAGCAAUC-GCGGCGA---AAUCGGAAC-UGG------GUGA--------------CCA-ACACCGGUU-GGAUG---AUUU-----GAGGAGCAUUUGAGUUUAUCCGGUCAGGCGGCU--GAGGAU-UGCCGCC-AUCCUAU-GCCUGGCCGGUU-GGCUCGA
URS0000D671E5_379731/1-124  UAGCAAUC-GCGGCGA---AAUCGGAAU-UGG------GUGA--------------CCA-ACACCGAUU-GGAUG---AUGU-----GAGGAGCAUUUGAGUUUAUCCGGCCAGGCGGCU--GAGGAU-UGCCGCC-AUCCUAU-GCCUGGCCGGUU-GGCUCGA
URS0000D6B105_1402579/1-123 UAGCAAUC-GCGGCGA---AAUCGG-AC-UGG------GUGA--------------CCA-ACACCGAUU-GGAUG---AUGU-----GAGGAGCAUUUGAGUUUAUCCGGCCAGGCGGUU--GAGGAU-UGCCGCC-AUCCUAU-GCCUGGCCGGUU-GGCUCGA
URS0000D6B105_1408193/1-123 UAGCAAUC-GCGGCGA---AAUCGG-AC-UGG------GUGA--------------CCA-ACACCGAUU-GGAUG---AUGU-----GAGGAGCAUUUGAGUUUAUCCGGCCAGGCGGUU--GAGGAU-UGCCGCC-AUCCUAU-GCCUGGCCGGUU-GGCUCGA
URS0000D6C8BD_12908/1-125   UAGCAAUC-GCGGCGA---AAUCGGAAC-UGG------GUGA--------------CUG-AGACCGAUU-GGAUA---AUGU-----GAGGAACAUUUGGGUUUAUCCGGCCAGGCGGCUU-GAGGAU-UGCCGCC-AUCCUAA-GCCUGGCCGGUU-GGCUCGA
URS0000D6C8BD_1211113/1-125 UAGCAAUC-GCGGCGA---AAUCGGAAC-UGG------GUGA--------------CUG-AGACCGAUU-GGAUA---AUGU-----GAGGAACAUUUGGGUUUAUCCGGCCAGGCGGCUU-GAGGAU-UGCCGCC-AUCCUAA-GCCUGGCCGGUU-GGCUCGA
URS0000D68502_12908/1-126   UAGCAAUC-GCGGCGA---AAUCGGAAC-UGG------GUGA--------------CUA-AGACCGAUU-GGAUG---AUGU-----GAGGAGCAUUUUGGUUUAUCCGGCCAGGCGGCUUAGGGGAU-UGCCGCC-AUCCUAA-GCCUGGCCGGUU-GGCUAAA
URS0000D6A0BA_1197721/1-126 UAGCAAUC-GCGGCGA---AAUCGGAUC-UGG------GUGA--------------CUG-AGACCGAUU-GGAUG---AUGU-----AAAGAGCAUUUUGGUUUAUCCGGCCAGGCGGCUUAGAGGAU-UGCCGCC-AUCCUAA-GCCUGGCCGGUU-GGCUAAA
URS0000D6CAFF_1189622/1-124 UAGCAGUU-GCGGCCUA--GUUCAUACAGCUU------GUAU---------------ACGUGUAUGGAU-GGAUA---GUGU-----GGGGAACAUUUAAGAUUAGCCGGUGAGGCGCUC---AGGAU-UGCCGCC-AUCCGA--GUCUCACCGGUU-GGCUUGA
URS0000D69C79_1204471/1-124 UAGCAGUU-GCGGCCUA--GUUUAUAUA----------GCUUGUAUACG-----------UAUAUGAAU-GGAUA---GUGU-----GGGGAACAUUUAAGAUUAGCCGGUGAGGCGCUC---AGGAU-UGCCGCC-AUCCGA--GUCUCACCGGUU-GGCUUGA
URS0000D6CD5A_12908/1-109   UAGCAAUACGCGGCCUA--GUCU---------------GAAA-----------------------AGAU-GGAUA---AUGU-----UUAGAGCAU-UAAGUUUAGCCGGUGGGGCGGUUU-CGGGAU-UGCCGCC-AUCCUA--GUCCCACCGGUU-GGCUUAU
URS0000D682AA_1215087/1-139 UAGCAGUU-GCGGCCUAG-UUCGCGCAG-ACCGUCCGCAUUA--------GUUGACGGGCCUAUGUGAGUGGAUA---GUGU-----GUGGAACAUUUAAGUUUAGCCGGUGGGGUAGCU--GUGGA-AUGCCGCCA-UCCUA--GCCUCACCGGUU-GGCUUAU
URS0000D67D4F_1191300/1-113 UAAUAGAUCGCGGCGU---GUGCC--------------UUUA----------------------GGGGCCAGAUGA--UUGG-----UUAGGCCAGUUAGUUAAAGCCCAAAGGGAUAUA--CGGAAA-GGCCGCA-UGUCCAC-UCCCUUUGGGUU-UUGCUAG
URS0000D68FAE_1136164/1-113 UAAUAGAUCGCGGCGU---GUGCC--------------UUUA----------------------GGGGCCAGAUGA--UUGG-----UUAGGCCAGUUAGUUAAAGCCCAAAGGGAUACA--CGGAAA-GGCCGCA-UGUCCAC-UCCCUUUGGGUU-UUGCUAG
URS0000D6C523_1201293/1-115 UAAUAUAU-GCGACGCGU-ACCUU--------------GAAA----------------------AAGGUCAGAUGA--UUGG-----UUAGGCCAGUUAGUUGAAGCCGGGGAGAAUAAUG-CAGAAA-GGUCGCU-UUUCUAU-UUAUCCUCGGUU-UUGCUAG
URS0000D691DB_12908/1-108   UAACAUUACGCGGCGAC--GU-----------------UUU--------------------------ACAAGAUGG--UUAC------UUAAGUAACUUGGUUAAGCCGAGGUAAGGCGAU-UGGAAU-UGCCGCA-GUUCUAAGUCUGCCUCGGUUUUGCUAG-
URS0000D6BCB0_991999/1-115  UAACAUGACGCGGCUA----GAGUU-------------UUAG---------------------GACUCGUGGAUGG--UUGU------UUUAACAACUUGGUUAAGCCGAGGUAAGGCGUG-AGGAAU-UGCCGCA-GUUCUAAGUCUGCCUCGGUUUUGCUAG-
URS0000D6BCB0_991944/1-115  UAACAUGACGCGGCUA----GAGUU-------------UUAG---------------------GACUCGUGGAUGG--UUGU------UUUAACAACUUGGUUAAGCCGAGGUAAGGCGUG-AGGAAU-UGCCGCA-GUUCUAAGUCUGCCUCGGUUUUGCUAG-
URS0000D6A57C_1191522/1-115 UAACAUGACGCGGCUA----GAGUU-------------UCAG---------------------GACUCGUGGAUGG--UUGU------UUUAACAACUUGGUUAAGCCGAGGUAAGGCGUG-AGGAAU-UGCCGCA-GUUCUAAGUCUGCCUCGGUUUUGCUAG-
URS0000D6C205_1191324/1-115 UAACAUGACGCGGCU----AGAGUU-------------UUAG---------------------GACUCGUGGAUGG--UUGU------UUUAACAACUUGGUUAAGCCGAGGUAAGGCGA--GAGGAAUUGCCGCAGUUCUAAG-UCUGCCUCGGUUUUGCUAG-
URS0000D69004_693974/1-111  UAACAUUACGCGGCAAC--GUC----------------UUAG------------------------GACAAAACGG--UUGU------UCAAACAACUUGGUUAAGCCGGAGUAGGACGU--GUGGAAUUGCCGCAGUUCUAAG-UCUGCUCCGGUUUUGCUAA-
URS0000D6912F_693971/1-111  UAACAUUACGCGGCAAC--GUC----------------UUAG------------------------GACAAAACGG--UUGU------UCAAACAACUUGGUUAAGCCGGAGUAGGACGU--GUGGAAUUGCCGCAGUUCUAAG-UCUGCUCAGGUUUUGCUAA-
URS0000D69985_407976/1-112  UAACAUUACGCGGCAAC--GUC----------------UUAG------------------------GACAAAACGG--UUGU------UUAAACAACUUGGUUAAGCCGGAGUAGGGCGU--GUGGAAUUGCCGCAGUUCUAAG-UCUGCUCCGGUUUUGCUAAU
URS0000D6CE79_1191061/1-137 AAACAUUU-GCGGUGAA--AUGCGCAAUUGGAUUC---UGUU-----------GAGUUC-UUUGUGUAUGAGAAGG--UUGG---AGAAAGACCACUUUGUUA-AGCCGGGGUGAUGUUUUUUUGAAU-GACCGCA-GUUCGAA-AUCGCCCCGGUU-UCACAAU
URS0000D674EB_956149/1-136  UAACAUUU-GCGGUGAA--AUGCACUUUGGAUUC----UUUU------------GAGUACCUAGUGUAUGAGAAGG--UUGG---AUAAAGACCACUUUGUUA-AGCCGGGGCGAUGUUUUUCUGAAU-GACCGCA-GUUCAAA-AUCGCCCCGGUU-UCACAAU
URS0000D663AC_1141661/1-138 UAACAUUU-GCGGUGAA--AUGCAC-UAUCGA------ACUAUUUAUAGG------UCAAUAUGUGUGUGAGAAGG--UUGG---AUAAAAACCACUUUGUUA-AGCCGGGGCAAUGUUUU-CUGAAC-GACCGCA-GUUCAAA-GUUGCUCCGGUU-UCACAAU
URS0000D67449_12908/1-137   UAACAUUU-GCGGUGAA--AUACACCUCUGACUU----ACUCUU----------AAAUCAGAGA-GUAUGAGAAGG--UUGG---AUAAAGACCACUUUGUUA-AGCCGGGGCAAUGUUUUUCUGAAC-GACCGCA-GUUCGAA-GUUGCCCCGGUU-UCACAAU
URS0000D6848D_1123863/1-130 UAACACUU-GCGGUGUG--GUCCAUAUCGG--------UUAGGU--------------UUGAUGUGGAUGAGAAG---GUCG--GAUAAAGGCCACUAAGUUA-AGCCGAGGAAGUGAGUUUGUGAAG-UGCCGCG-AUUCAAU-CACUCCUCGGUU-UUGCUAA
URS0000D65A2D_484021/1-135  UAACAUUU-GCGGCGAG--GUUCACAAUUUGUAU----UUAG------------GUACUGAUUGUGGAUGAGAAGG--UUGG---AGAAAGACCACUUGGUUA-AGCCGGAGGAUGUGUCC-UAGAAU-UGUCGCU-AUUCUGU-CAUCCUCCGGUU-UUGCUAA
URS0000D65A2D_12908/1-135   UAACAUUU-GCGGCGAG--GUUCACAAUUUGUAU----UUAG------------GUACUGAUUGUGGAUGAGAAGG--UUGG---AGAAAGACCACUUGGUUA-AGCCGGAGGAUGUGUCC-UAGAAU-UGUCGCU-AUUCUGU-CAUCCUCCGGUU-UUGCUAA
#=GC SS_cons                ::::::::.AAAAA:::..<<<<<<.............____...................._>>>>>>:::::::..<<<<....._____>>>><<<<<<<---<<<<<<<<<<-----.-<<<<<._aaaaa_.>>>>>--.>>>>>>>>>>--.>>>>>>>
#=GC RF                     UAACAuUu.GCGGCgaa..gccccc.............uUaa....................agggggcuaGAUGG..gUGc.....aaagAgCAcuugggcauAgCCGggggggcgguUu.aaGGAu.uGCCGCa.aUCCuAu.gccccccCGGUU.ugcccaa
//
