# STOCKHOLM 1.0
#=GF ID HTH-XRE
#=GF AC RF02923
#=GF DE HTH-XRE RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 49.8
#=GF NC 40.5
#=GF TC 50.6
#=GF SE Weinberg Z
#=GF SS Published; PMID:28977401;
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 26.51 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory_region;
#=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. Downstream gene
#=GF WK HTH-XRE_RNA_motif
#=GF SQ 60

URS0000D676F5_12908/1-86   GAUCAGCAAUAGGGCAUAGGUGACACAAGGCAGUUGUCACGACG-GAACUCUGUGCCC----GGAAGACUUGCAAAGGU-ACUUUCCCUUCC
URS0000D65A88_12908/1-84   GAUCAGCAGUGUGGUAUAGGCGGC-UUGGACAGU-GCCGCAUCG-GAACUCUAUACCC----GGAAGACUUGCAAAGGUG-AUUUCCCUUCC
URS0000D68664_12908/1-86   GAUCAGCACAGUGGUGCAGGUGACACAGGGCAGUUGUCACAUCG-GAACUCUGCACCC----GGAAGACUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6CB6E_12908/1-86   GAUCAGCACAGUGGUGUAGGUGACACAGGGAAGUUGUCACAUCG-GAACUCUGCACCC----GGAAGACUUGCAAAGGUG-AUUUCCCUUUC
URS0000D69B40_12908/1-86   GAUCAGCACAGUGGUGUAGGUGACACAGGGAAGUUGUCACAUCG-GAACUCUGCACCC----GGAAGACUUGCAAAGGUG-AUUUCCAUUUC
URS0000D6CF07_12908/1-82   AAUCAGA-----AGUGUAGGUGACACAGGGCAGUUGUCACAUCG-GAACUCUGCACCC----GGAAGACUUGCAAAGGUGGACAGAUUGUUU
URS0000D6A795_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGCUCUAUUAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D697C8_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGCUCAAAUAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D6C872_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGCUCGAAUAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D6BD0B_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGUUCUAGUAAUGGGCUUACGAAGGUUGAUUUCCCUUUC
URS0000D69611_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGUUCUAGUAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D68A58_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGCUCAAGUAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D670FF_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACUG---GGCGCAUCG-GAACUUCCGGCUCAAGUAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D6BF31_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGCUCUAGAAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D6CF48_12908/1-84   GAUCAGC---AAUGUCGGAGCGUC-AGGACAG---GGCGCAUCG-GAACUUCCGGCUCUAGUAAUGGGCUUGCGAAGGUUGAUUUCCCUUUC
URS0000D68EFD_12908/1-76   GAUCAGC---ACUGUUGGGGCAGA-UAAAU-----UCUGUAACG-GAACUCCCAACU-----GGAAGACUUGCAAAGGUG-AUUCCCUUUCC
URS0000D683C9_12908/1-82   GAUCAGCU--AUUGUCAGGGCAGUGAAAGACAG-CACUGCGACG-GAACUCCUGGCA-----GGAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6C931_12908/1-82   GAUCAGCU--AUUGUCAGGGCAGUGAGAGACAG-UACUGCGACG-GAACUCCUGGCA-----GGAAGGCUUACAAAGGUG-AUUUCCCUUUC
URS0000D6B223_12908/1-82   GAUCAGCU--AUUGUCAGGGCAGUGAGAGACAG-UACUGCGACG-GAACUCCUGGCA-----GGAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D672A4_12908/1-76   GAUCAGC---ACUGCCAGGGCAUU-GUUG------GAUGCGUCG-GAACUCCUGACA-----GAAUAGCUUGCGAAGGUUUAUUCCCUUUCC
URS0000D6BDF3_12908/1-75   GAUCAGC---ACUGCCAGGGCAUC-UUUG------GAUGCGUCG-GAACUCCUGACA-----GAAUAGCUUGCGAAGGUUUAUUCCCUUUC-
URS0000D6B6E1_12908/1-75   GAUCAGC---ACUGCCAGGGCAUC-GUUG------GAUGCGUCG-GAACUCCUGACA-----GAAUAGCUUGCGAAGGUUUAUUCCCUUUC-
URS0000D67D72_12908/1-82   GAUCAGCAU-UAGGUUGGGGUAUACAAGACGG--GUAUGCAUCG-GAACUCCCACCA-----GGUAAGCUUGUAAAGGUG-AUUCCCUUUUC
URS0000D67599_483218/1-76  GAUCAGC---AUCGCUGGGGAAUGGAAUA-----CCAUUCAUCG-GAACUCCCGGC------ACAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6AB52_12908/1-74   GAUCAGC---AUAGCCGGGGAAUGUGCAU-----ACAUUCAUCG-GAACUCCCGGC--------AAGUCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6AF21_12908/1-74   GAUCAGC---AUAGUCGGGGAAUGUGCAU-----ACAUUCAUCG-GAACUCCCGGC--------AAGUCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6B0E9_12908/1-78   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCGGGAACUCCCGGC------AAAAGGCUUGCAAAGGGUGAUUUCCCUUUC
URS0000D675A2_12908/1-74   GAUCAGC----AGGCCGGGGAAUGUGCAU-----ACAUUUAUCG-GAACUCCCGGC-------AAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D68937_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGUGCAU-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6BAF2_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AACAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D678F8_12908/1-76   GAUCAGC---AAAGCCGGGGGAUGUGCAG-----ACAUUCAUUG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D66E56_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUUG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6D388_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGCGCAG-----ACAUUCAUCG-GAACUCUCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D661B4_12908/1-75   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCUCGG-------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6D23A_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCUCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6AEE3_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCUGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6C948_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGA------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6B076_1235802/1-76 GAUCAGC---AAAGCCGAGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6C246_657318/1-76  GAUCAGC---AAAGCCGGGGAAUGUGCAG-----AUAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6A704_12908/1-76   GAUCAGC---AAAGUCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6994F_1262758/1-76 GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6994F_12908/1-76   GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6994F_500632/1-76  GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6994F_411486/1-76  GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6994F_657317/1-76  GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6994F_742765/1-76  GAUCAGC---AAAGCCGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6C79E_12908/1-76   GAUCAGC---AAAGAUGGGGAAUGUGUAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6894E_12908/1-76   GAUCAGC---AAAGCUGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAUAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6AE82_12908/1-76   GAUCAGC---AAAGCUGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6AE82_718255/1-76  GAUCAGC---AAAGCUGGGGAAUGUGCAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6B819_12908/1-77   GAUCAGC---AAAGCUGGGGAAUGUGUAG-----ACAUUCAUCG-GAACUCCCGGCA-----AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6C4DE_12908/1-76   GAUCAGC---AAAGCUGGGGAAUGUGUAG-----ACAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D65DB8_12908/1-74   GAUCAGC----AGGCCGGGGAAUGUGCAU-----ACAUUCAUCG-GAACUCCCGGC-------AAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6ABBC_12908/1-76   GAUCAGC---AAAGACGGGGAAUG-CGCAGA----CAUUCAUCG-GAACUCCCGGC------AAAAGGCUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6D2F6_12908/1-77   GAUCAGCA--UAUGCAGGGGCAUA-CAUUG-----UAUGUGACG-GAACUCCCAGCA-----GGAAGACUUGCAAAGGUG-AUUUCCCUUUC
URS0000D6C569_12908/1-77   GAUCAGCA--UAAGCAGGGGCAUA-CAUUG-----UAUGCGACG-GAACUCCCGGCA-----GGAAGACUUGCAAAGGUG-AUUUCCCUUUC
URS0000D67585_12908/1-80   GAUCAGCA--UAUGCAGGGGCAUA-CAUAG-----UAUGCGUCG-GAACUCCCGGCAGUA--AGAAGACUUGCAAAGGUG-AUUUCCCUUUC
URS0000D693C5_12908/1-79   GAUCAGCA--AAUGCUGGGGCAUAUGUUGG----AUAUGCGACG-GAACUCCCGGCA-----AAACAGCUUGCAAAGGUG-AUUCCCUUUUC
URS0000D667E7_411489/1-78  GAUCAGCA--UUUACCGGGGCAUACGAGAG----GUAUGCG-CG-GAACUCCCGGCA-----AGCAAGCUUGCAAAGGUG-AUUCCCUUUUC
URS0000D667E7_12908/1-78   GAUCAGCA--UUUACCGGGGCAUACGAGAG----GUAUGCG-CG-GAACUCCCGGCA-----AGCAAGCUUGCAAAGGUG-AUUCCCUUUUC
#=GC SS_cons               :::::::...::<<<<<<<<<<<<<_____....>>>>>>----.----->>>>>>>.....::::::::::::::::::.:::::::::::
#=GC RF                    GAUCAGC...AauGccgGGGcgugugaagg....acacgCAUCG.GAACUCCcggCa.....aaAAGGCUUGCAAAGGUG.AUUUCCcUUUC
//
