# STOCKHOLM 1.0
#=GF ID RAGATH-28
#=GF AC RF03052
#=GF DE RAGATH-28 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 45.3
#=GF NC 42.0
#=GF TC 45.7
#=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 28.14 -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 85

URS0000D67B13_1262848/1-83 AGAG--GGUUGAUUCGUCCC-CUCUCGCUGCGGUUGUCGU---UAUAGC---UCCGUACAAUGUCAGCU-----AACC------------AGCUGGCAU-AUGGCGG-AGC
URS0000D67D5D_12908/1-80   GCAG--AGUUGAUUCGUCCU-CUGUCGCGGCAACUGCUGU---CAUAGC---UCCGUACACUGUCAA-------UACUU-------------UUGACAG-AUGGCGG-AGC
URS0000D65DF0_12908/1-96   UGGG--GAUUGAUUCGUCUC-CUCGGAGGGAACGG-CUG---ACAUAUU--GCAGGAACACAGCAACCUAAUUUCCGAACA----AAAUCAGGUUGCUG-GGGGCGA-AGC
URS0000D6C5B8_12908/1-96   UGAG--GAUUGAUUCGUCUC-CUCAGAGGGAACGG-C---UGACAUACU--GCAGGAACACAGUAACUUAAUUUCCGAACA----AAAUCAGGUUGCUG-GGGGCGA-AGC
URS0000D6A8A0_12908/1-96   UGAG--GAUUGAUUCGUCUC-CUCGGAGGGAACGG-CU---GACAUACU--GCAGGAACACAGUAACUUAAUU-GCCGAACAA---AAUCAGGUUGCUG-GGGGCGA-AGC
URS0000D6AD23_663278/1-86  GGGC--GGUUGAUUCGUCCC-AAACCGGGUGCCGG-AGG-UGAGAUGGA--CCAAGAGAACCGGGGCUU-----UUGA------------AAGCCGCGGGAUGGCGA-AGC
URS0000D6AF59_485916/1-80  ACAU--GUUUGAUUCGUCGC-AUGCCAGGUAAAUGGUUUUUAUAGUAUU----GGGGAAACCGGAU--------GAAAA--------------AUCCGG-GUGGCGA-AGC
URS0000D68C34_12908/1-86   GCCA-UGCUUGACUCGUCGCAUGACCGGAUUGAAAGGGGUUAGGUUACC--UGGGGCAAACCGGAUGA------UUA--------------UCAACCGG-GUGGCGA-AGC
URS0000D673A9_12908/1-83   CUCG-UGUUUGAUUCGUCGCAUGGCCGGGUUGAAAGGGGUAAA-AGCUG--GGGUGACGACCGGAU--------GAAAA--------------AUCCGG-GGGGCGA-AGC
URS0000D683E6_12908/1-82   GUAC--GGUUGAUUCGUCCC-GUUCCGAUCGGCGCAGGAG---CAUAAG-----AAAAAACAGCUUUUU-----AGAC------------AAAAUGCUGAAUGGCGG-AGC
URS0000D6CB25_12908/1-84   GUAC--GGUUGAUGCGUCCC-GUACCGAUCGGCGCAGCGGA---AUAUA-----CAAAAACGGCUUUUUA----AAAC-----------UGAAUUGCCGAAUGGCGA-AGC
URS0000D68F6F_12908/1-84   GUAC--GGUUGAUGCGUCCC-GUACCGAUCGGCGCAGCGGAAU---AUA-----UAAAAACGGCUUUUUA----AAAC-----------UGAAUUGCCGAAUGGCGA-AGC
URS0000D680F7_213810/1-85  CCGG--GGUUGAUACGUCCC-CCGGUGUCGCACAGGAUUG---CAUGAU---GCCAGUCACCUGAUUUCA----ACC------------UGGAAUCAGGAAUGGCGG-AGC
URS0000D6D0BC_1262956/1-85 CCGG--GGUUGAUACGUCCC-CCGGUGUCGCGCAGGAUUG---CAUGAU---GCCAGCCACCUGAUUUC-----AACCC-----------GAAAUCCGGAAUGGCGG-AGC
URS0000D6C733_12908/1-85   CCGG--GGUUGAUACGUCCC-CCGGUGCCGCACAGGAUUG---CAUGAU---ACCAGCCACCUGAUUUC-----AACUC-----------GAAAUCCGGAAUGGCGG-AGC
URS0000D6C1D6_12908/1-85   CAGAACGGUUGAUUCGUCCCGGCUGAUGAGCGAGUGUG-----UAUACG-----UCAAAACGGAAUUU------GAGAUACA---------AAAUUCCGAAUGGCGG-AGC
URS0000D6774A_12908/1-86   CAGAACGGUUGAUUCGUCCCGGCUGAUGAGCGAGUGCG-----UAUACA----UCGGAAACGGAAUUU------GAGAUACA---------AAAUUCCGAAUGGCGG-AGC
URS0000D65BAD_12908/1-94   ACAU-CGGUUGAUUCGUCCCGAUGCAGAAGCGUAUACAG----CAUAGU-----ACAGAACGGAUUUAGCUUC-AAAAAUCA----GAAG-UAAUUCCGAAUGGCGA-AGC
URS0000D65FFD_12908/1-85   AGCG--GAUUGAUUCGUCUC-UGCUUGAUGUGAC-ACGGCUGACAUACA--GCAAAGCUACCGAUAAC------CUCAA------------GUUAGCGG-AUGGCGG-AGC
URS0000D67940_12908/1-85   GGCG--GAUUGAUUCGUCUC-UGCUUGAUGUGA-CACGGCUGACAUACG--GCAAAGCUACCGAUAAC------CUCAA------------GUUAGCGG-AUGGCGG-AGC
URS0000D67AAE_12908/1-83   GGCG--GAUUGAUUCGUCUC-CACCCGAUGCAACGGCUGA---CAUACG--GCGAAGUCACCGAUAACC-----UCA-------------GGUUAGCGG-AUGGCGA-AGC
URS0000D6726C_12908/1-83   GACG--GAUUGAUUCGUCUC-CGCCCGAUGCAACGGCUGA---CAUACG--GCGAAGUCACCGAUAACC-----UCA-------------GGUUAGCGG-AUGGCGA-AGC
URS0000D6ACC7_12908/1-83   GGCG--GAUUGAUUCGUCUC-CGCCCGAUGCAACGGCUGA---CAUACG--GCGAAGUCACCGAUAACC-----UCA-------------GGUUAGCGG-AUGGCGA-AGC
URS0000D6C9A8_12908/1-81   AGCG--GAUUGAUUCGUCUU-CGCUUGAUGAAUGGUUGUU----AUACA----CUUAGCACCGAUAAC------ACCAAA-----------GUUAGCGG-AUGGCGA-AGC
URS0000D68686_12908/1-81   AGCG--GAUUGAUUCGUCUU-CGCUUGAUGAAUGGUUGUU----AUACA----CUUAGCACCGAUAAC------AUCAAA-----------GUUAGCGG-AUGGCGA-AGC
URS0000D6B4DA_12908/1-84   GCCU--GGUUGAUUCGUCCU-GGGCUGUGGAGCAGGUG---AACAGAUG---CGGAAAACCUGGGC-CCA----AUG------------UGGCGGUCGGAAUGGCGA-AGC
URS0000D6BE6A_12908/1-85   GGCC--GGUUGAUUCGUCCC-GGCCUGUGGAACGGGUGAA---CAGGAG--ACGGAAACCCCGA--GCC-----AAAUGC----------GGCGGUCGGAAUGGCGA-AGC
URS0000D67ACC_12908/1-87   GAGC--GGUUGAUUCGUCCU-GCAUGUGGAAAUUGGCGGACAUAAGAAA--GGCAAAAAGCCGAGA--------AAUCAUAAAA---------UCUCGG-AUGGCGA-AGC
URS0000D6D015_12908/1-86   AAAC--GGUUGAUUCGUCCU-GUGAGCGGAAAUUGGUGGUUAA-AUAGC--AUGAACUAUCCUAGA--------AAACAAAAUA---------UCUGGG-AUGGCGA-AGC
URS0000D66B52_12908/1-86   AAAC--GGUUGAUUCGUCCU-GUAAGCGGAAAUUGGUGGUUAA-AUAGC--AUGAACUAUCCUAGA--------AAAUAAAAUA---------UCUGGG-AUGGCAA-AGC
URS0000D65978_12908/1-84   AAGA--GGUUGAUUCGGCCC-GCCUGGGGAGACCGGGGGA---AAUACG-GGUGAAAUAACCGGGCUG------AAUGA------------CAGGCUGG-GUGGCGA-AGC
URS0000D68437_445972/1-84  AGGC--GGUUGAUUCGUCCC-GCCUGGGGAGGCCGGUGGA---AAUACG-GGCGAAAUAACCGGGCUG------AAUGA------------CAGGCUGG-GUGGCGA-AGC
URS0000D664A7_12908/1-84   AGGC--GGUUGAUUCGUCCC-GCCUGGGGAGACCGGUGGA---AAUACG-GGUGAAAUAACCGGGCUG------AAUGA------------CAGGCUGG-GUGGCGA-AGC
URS0000D6754D_12908/1-84   AGGC--GGUUGAUUCGUCCC-GCCUGGGGAGGCCGGUGGAAAU---ACG-GGUGAAAUAACCGGGCUG------AAUGA------------CAGGCUGG-GUGGCGA-AGC
URS0000D65F83_12908/1-85   AGGC--GGUUGAUUCGUCCC-GCCUGGGGAGGCCGGUGGA-AAUACAGU--GCAAAAGAACCGGGCUG------AACAG------------CAGGCUGG-GUGGCGA-AGC
URS0000D65F83_552398/1-85  AGGC--GGUUGAUUCGUCCC-GCCUGGGGAGGCCGGUGGA-AAUACAGU--GCAAAAGAACCGGGCUG------AACAG------------CAGGCUGG-GUGGCGA-AGC
URS0000D65C9D_12908/1-85   AGGC--GGUUGAUUCGUCCC-GCCUGGGGAAUCCGGUGGA-AAUACAGG--GCGAAAGAACCGGGCUG------AACAG------------CAGGCUGG-GUGGCGA-AGC
URS0000D656F9_12908/1-85   AGGC--GGUUGAUUCGUCCC-GCCUGGGGAGACUGGUGGAAAU-AUCGG--GCAAAAGAACCGGGCUG------AACAA------------CAGGCUGG-GUGGCGA-AGC
URS0000D6C187_12908/1-88   ACGUCUGGUUGAUUCGUCCCAGCGUGGCUA--AGGGACGGA--CAUAAU--GAGAAGGAACUGAGCAGA-----AAAAUG----------UCUGGUUGG-GUGGCGA-AGC
URS0000D658DC_12908/1-88   GACC--GGUUGAUUCGUCCC-GGUUGUGUU--CGGGACGCAGGCAUAAA--GAAAAGGAACUGAGCAG------AAAAGGACG--------CUGGUCGG-GUGGCGA-AGC
URS0000D666C8_12908/1-88   GACC--GGUUGAUUCGUCCC-GGCUGCGUU--CGGGACGCAGGCAUAAA--GAAAAGGAACUGAGCAG------AAAAGGACG--------CUGGUCGG-GUGGCGA-AGC
URS0000D6C4F6_12908/1-88   GACC--GGUUGAUUCGUCCC-GG--CUGUGUUCGGGACGCAGGGAUAAA--GAAAAGGAACUGAGCAG------AAAAGGACG--------CUGGUCGG-GUGGCGA-AGC
URS0000D6CD48_12908/1-88   GACC--GGUUGAUUCGUCCC-GG--CUGUGUUCGGGACGCAGGCAUAAA--GAAAAGGAACUGAGCAG------AAAAGAACG--------CUGGUCGG-GUGGCGA-AGC
URS0000D69098_12908/1-88   GACC--GGUUGAUUCGUCCC-GG--CUGUGUUCGGGAUGCAGGCAUAAA--GAAAAGGAACUGAGCAG------AAAAGGACG--------CUGGUCGG-GUGGCGA-AGC
URS0000D69E69_12908/1-88   GACC--GGUUGAUUCGUCCC-GG--CUGUGUUCGGGACGCAGGCAUAAA--GAAAAGGAACUGAGCAG------AAAAGGACG--------CUGGUCGG-GUGGCGA-AGC
URS0000D69E69_665940/1-88  GACC--GGUUGAUUCGUCCC-GG--CUGUGUUCGGGACGCAGGCAUAAA--GAAAAGGAACUGAGCAG------AAAAGGACG--------CUGGUCGG-GUGGCGA-AGC
URS0000D6665A_12908/1-87   CAGA-CGGUUGAUUCGUCCCG-GUGCAGGAAGCGCG---CGGACAUAAG--GAAACGGAACCAAGCGGG-----AAAAG-----------CCCGGUCGGGAUGGCGA-AGC
URS0000D67BA0_999408/1-88  GCAGACGGUUGAUUCGUCCCGGUGCAGGAAACGCG-UGGA---CAUAAG--GAAACGGAACCAAGCAGG-----AAAUA-----------CCUGGUCGGGAUGGCGG-AGC
URS0000D67DC4_742733/1-88  GCAGACGGUUGAUUCGUCCCGGUGCAGGAAGCGCG-CGGA---UAUAAG--GAAACGGAACCAAGCGGG-----AAAAG-----------CCCGGUCGGGAUGGCGA-AGC
URS0000D663C1_997897/1-88  GCAGACGGUUGAUUCGUCCCGGUGCAGGAAGCGCG-CGGA---CAUAAG--GAAACGGAACCAAGCGGGC----AAU------------GCCCGGUCGGGAUGGCGA-AGC
URS0000D6CBCC_12908/1-85   GCAGACGGUUGAUUCGUCCCGCUGCAGGAAGCCGU-----GGACAUAGG--GAACAGGAACUGAGCAGG-----AUAA------------CCUGGUCGG-GUGGCGG-AGC
URS0000D6BB68_12908/1-85   GCAGGCGGUUGAUUCGUCCCGCUGCAGGAAGCCGU-----GGACAUAGG--GAACAGGAACUGAGCAGG-----AUAA------------CCUGGUCGG-GUGGCGG-AGC
URS0000D6CB12_12908/1-90   GCAUACGGUUGAUUCGUCCCGAUGCCGGAAGCUG-GCGG---ACAUAGA--GAAAGGGAACUGAGCAG------AAAAAGUACA-------CUGGUUGG-GUGGCGA-AGC
URS0000D688F9_12908/1-90   GCAUACGGUUGAUUCGUCCCGAUGCCGGAAGCUGG-CGG---ACAUAGA--GCAAGGGAACUGAGCAG------AAAAAGUACA-------CUGGUUGG-GUGGCGA-AGC
URS0000D6CC97_12908/1-90   GCAUACGGUUGAUUCGUCCCGAUGCCGGAAGCUGG-CGG---ACAUAGA--GAAAGGGAACUGAGCAG------AAAAAGUACA-------CUGGUUUG-GAGGCGA-AGC
URS0000D6C5C4_12908/1-86   UGGA--GGUUGAUGCGUCCC-UCCCGCCGUGAGC-GAGGGACACAUUGA---GUAAAGAACCGGGC--------AGAAAUCGGGG--------GCCUGG-GUGGCGA-AGC
URS0000D6C001_12908/1-82   GCGG--GGUCGAUUCGUCCC-CCGCCCGUGGCCAUGGCGGG--CAUAGAAGGGGAUAAACCGGGCG--------GAAA---------------CGGCCGUAUGGCGA-AGC
URS0000D693E7_665956/1-81  GCGG--GGU-GAUUCGUCCC-CCGCCCGUGGCCAUGGCGG--GCAUAGA-GGGGUAAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D693E7_12908/1-81   GCGG--GGU-GAUUCGUCCC-CCGCCCGUGGCCAUGGCGG--GCAUAGA-GGGGUAAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D6C685_12908/1-82   GCGG--GGUCGAUUCGUCCC-CCGCCCGUGGCCAUGGCGGG--CAUAGA-AGGGGAUAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D670E7_665956/1-82  GCGG--GGUCGAUUCGUCCC-CCGCCCGUGGCCAUGGCGGACACAGAGG---GGUAAAAACCGGACG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D68FBB_12908/1-83   GCGG--GGUUGAUUCGUCCC-CCGCCCGUGGCCAUGGCGGGCAUAGAGG--GGGUGAAAACCGGGCG-------GAAA--------------CGGUCGG-AUGGCGA-AGC
URS0000D67B83_12908/1-82   GCGG--GGU-GAUUCGUCCC-CCGCCCGUGGCCAUGGCGGGCAUAGAGG--GGGUGAAAACCGGGCG-------GAAA--------------CGGUCGG-AUGGCGA-AGC
URS0000D6C39D_12908/1-83   GCGG--GGUUGAUUCUUCCC-CCGCCCGUGGCCAUGGCGGGCAUAGAGG--GGGUGAAAACCGGGCG-------GAAA--------------CGGUCGG-AUGGCGA-AGC
URS0000D6CDE2_12908/1-80   ACAG--GGUCGAUUCGUCCC-CUGCGGAUG---GUCUGGCAGGCAUAGC--GGCAAAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D682F0_12908/1-80   ACAG--AGUUGAUGCGUCCC-CUGUGGAUUGCCCGGCGGG---CAUAGC--AGCGAAAAUCCGGGCU-------GAAA--------------AGGCCGG-AUGGCGA-AGC
URS0000D6CD57_12908/1-80   ACAG--GGUCGAUUCGUCCC-CUGCGGAUUGCCCGGCGGG---CAUAGC--AGCAAAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D6D222_12908/1-80   ACAG--GGUCGAUUCGUCCC-CCGUGGAUGACCUGGCGGG---CAUAGC--AGCAAAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D6696C_12908/1-80   ACAG--GGUCGAUUCGUCCC-CUGCGGAUGGUCUGGCAGG---CAUAGC--GGCAAAAAACCGGGCG-------GAAA--------------CGGCCAG-AUGGCGA-AGC
URS0000D6CB2E_12908/1-81   ACAG--GGUCGAUUCGUCCC-CUGCGGAUUGCCCGGCGGG---CAUAGC-AGCGAAAAAACCAGGCU-------GAAA--------------AGGCUGG-AUGGCGA-AGC
URS0000D66C6A_12908/1-82   GCGG--GGUUGAUUCGUCCC-CUGCGGAGCGAGCGGCGGG---CAUAAGGCAAGAGAAAGCCGGGCA-------GAAA--------------UGGCCGG-AUGGCGA-AGC
URS0000D69FE8_12908/1-80   CCGG--GGUUGAUACGUCCU-CCGGAGCGUGACCGGCGGG---AAUAAA--GGGAAAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D67DD9_12908/1-80   CCGG--GGUUGAUACGUCCU-CCGGAACGUGACCGGCGGG---CAUAGA--GGGAAAAAACCGGGCG-------AAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D6CE68_12908/1-81   CCGG--AGUUGAUACGUCCU-CCGGAGCGUGACCGGCGGGUAU-AGAAG---GGUGAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D65E86_12908/1-81   CCGG--GGUUGAUACGUCCU-CCGGAGCGUGACCGGCGGGCAU-AGAGG---GGUGAAAACCGGGCG-------AAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D6A974_12908/1-81   CCGG--GGUUGAUACGUCCU-CCGGAGCGUGACCGGCGGGCAU-AGAGA---GAUGAAAACCGGGCG-------GAAA--------------CGGCCGG-AUGGCGA-AGC
URS0000D68F3C_12908/1-82   GCGG--GGUCGAUUCGUCCC-CCGCGGCGUGACCGGCGGGCAU-AGAAG--AGCGGGAAGCCAGGCU-------GAAA--------------GGCCCGG-AUGGCGA-AGC
URS0000D65AAA_12908/1-82   GCGG--GGUCGAUUCGUCCC-CCGCGGCGUGACCGGCGGGCAU-AGAAG--AGUGGAAAGCCAGGCU-------GAAA--------------GGCCCGG-AUGGCGA-AGC
URS0000D67AF4_12908/1-81   GGGC--GGUUGAUGCGUCCC-GCGCGGUACGAUCUGGUGG--ACAUAUG-GGGCAUUCUGCGGGCC--------GAUUA--------------GGCCCG-AUGGCGG-AGC
URS0000D66B91_12908/1-81   GGGC--GGUUGAUGCGUCCC-GCGCGGUACAAGCCGGAG--GACAUAUG-GGGUGCUGCAC-GGGC--------CGGAUC-------------GCCCCG-GUGGCGG-AGC
URS0000D6A14F_12908/1-81   GGGC--GGUUGAUGCGUCCC-GCGCGGUACGAGCCGGAG--GACAUAUG-GGGUGCUGCACGGGCCG-------GAU---------------CGGCCCG-GUGGCGG-AGC
URS0000D688B3_12908/1-80   GGGC--GGUUGAUGCGUCCC-GCGCGGUACGAGCCGGAGGA--CAUAUG--GGCGCUACACGGGCCG-------GAU---------------CGGCCCG-GUGGCGG-AGC
URS0000D6C498_12908/1-85   GUGU--GGUUGAUUCGUCCC-ACACGCCAACGAGG----GAAAAAUAAA---ACACAAAACACAGCCGA-----AAAUA-----------UCGGGUGUGAAUGGCGGUAGC
URS0000D6C91D_12908/1-86   UAAG--AGUUGAUUCGUCCU-CUUAUUUGAAGUUUGAGG---ACAUAAA--AAAGGCGAAUUCAAUCA------UAAAUACU---------UGAUUGAA-UCGGCGA-AGC
URS0000D6C8D1_12908/1-83   GAUU--UGUUGAUUCGUCCG-AAUCUUAAAAAGCUAUA-CGGACAUAAA--AAAACAUACUUGGAU--------AUCAAAA------------AUCCAA-GUGGCGA-AGC
#=GC SS_cons               <<<<..<<__________>>.>>>>:::::::::::::::.::::::::..:::::::::<<<<<<<<......_____............>>>>>>>>.:::::::.:::
#=GC RF                    gcgg..GGUUGAUUCGUCCC.ccgccGguggaccgGugGg.aaCAUAaa..GgaaaaaAACcGgacgg......aAaAa............ccgucCgG.AUGGCGA.AGC
//
