# STOCKHOLM 1.0
#=GF ID RAGATH-15
#=GF AC RF03150
#=GF DE RAGATH-15 RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 199.5
#=GF NC 198.2
#=GF TC 214.5
#=GF SE Published; PMID:26167874;
#=GF SS Published; PMID:26167874;
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 26167874
#=GF RT New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT analysis.
#=GF RA Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL Nat Chem Biol. 2015;11:606-610.
#=GF CC RNA motif Associated with Genes Associated with Twister and Hammerhead
#=GF CC ribozymes (RAGATH).
#=GF WK RAGATH_RNA_motifs
#=GF SQ 14

URS0000D6ADD5_12908/1-306 UUGUUAGCUAGCAAUC--CCAUCGCUAAGGAGAAGC-AUGGGCUCACGGG-CUAUA--------CCUGUGAUGUAAAACCCACAUACUAUACUACAUUGCACUGUGUACUAGUAUGGAUAGGGCACUAAUCUUUA-CUCUAU--UUAGUGCAAA-ACUA----UAAUU-UCUC---GU---ACAACAUAAA-AUGUGAA-
URS0000D68018_12908/1-295 AGAGUAGCU-CUCUAUU-UCUUAGUGAAGG-CAAACUAAGG--GUGCAUU-AUAA---------AAUGUAU--GGUAUUCCGCAUAUUGGCUU----UGCG----AAGUCGAUAUGGACAGGACAUAGUUAAAUUGC--AAAUAACUAUGCAAGUAUUACUA-UUUCC-------CAGA--ACGUUAUGUA-ACGU-AC-
URS0000D658A7_12908/1-295 AGAGUAGCU-CUCUAUU-UCUUAGUGAAGG-CAAACUAAGG--GUGCAUU-AUAA---------AAUGCAU--GGUAUUCCGCAUAUUGGCUU----UGCG----AAGUCGAUAUGAACAGGACAUAGUUAAAUUGC--AAAUAACUAUGCAAGUAUUACUA-UUUCC-------CAGG--ACGUUAUGUA-AUGU-GC-
URS0000D65CDC_12908/1-295 AGAGUAGCU-AUCUAUU-UCUUAGUGAAGG-CAAACUAAGG--GUGCAUU-AUAA---------AAUGCAU--GGUAUUCCGCAUAUUGGCUU----UGCG----AAGUCGAUAUGGACAGGACAUAGUUAAAUUGC--AAAUAACUAUGCAAGUAUUACUAUUUUCC--------AGG--ACGUUAUGUA-ACGU-GC-
URS0000D67BD7_12908/1-295 AGAGUAGCU-AUCUAUU-UCUUAGUGAAGG-CAAACUAAGG--GUGCAUU-AUAA---------AAUGCAU--GGUAUUCCGCAUAUUGGCUU----UGCG----AAGUCGAUAUGGACAGGACAUAGUUAAAUUGC--AAAUAACUAUGCAAGUAUUA----CUAUU-UCCC---AGG--ACGUUAUGUA-ACGU-GC-
URS0000D6A8E5_12908/1-301 AGGGUAGCU-CCCUAU--UCUUAGCUAAGG-CAAACUAAGA--GCACAU--AUUGAUC-------GUGUGUA-GCAAAUCCACAUAACAACUGU-AUUGCG---GCAGUCGGUAUGGAUGGGACAUAGGUAGUAUAAUCAAGUGCCUAUGCAAGUAUUACUA-UUUUC-C-AGGA---------CGGCACGCCC-----U
URS0000D693F1_12908/1-301 AGGGUAGCU-CCCUAU--UCUUAGCUAAGG-CAAACUAAGA--GCACAU--AUUGAUC-------GUGUGUA-GCAAAUCCACAUAACAACUGU-AUUGCG---GCAGUCGGUAUGGAUGGGACAUAGGUAGUAUAAUCAAGUGCCUAUGCAAGUAUUACUA-UUUUC-C-AGGA---------CGGCACACCC-----U
URS0000D66CCC_12908/1-290 GGGAAACG--ACCCA---UCUUGGUGCAGG-CGAGCCAAGA--AUGCGUU-UUAAC--------AACGUAU---CCUUUCCACAUACUAUUUGC-AUUGCACA-GC-GAUAGUAUGGAUGGGACAUUGGUAUUUA-C---AGUACUAAUGCAAAUACUGUAUUUUUCU-A-UAUA---------GUGCGCA-A------U
URS0000D6729B_12908/1-290 GGGAAACA--ACCCA---UCUUGGUGCAGG-CGAGCCAAGA--AUGCGUU-UUAAC--------AACGUAU---CCUUUCCACAUACUAUUUGC-AUUGCACA-GC-GAUAGUAUGGAUGGGACAUUGGUAUUUA-C---AGUACUAAUGCAAACACUGUAUUUUUCU-A-UAU--A----AUGC-G----CA-AU----
URS0000D6B0F1_12908/1-291 AGGGUGGCU-ACCUUAU-UCUUGGCUAAGG-CAAACCAAGA--GUAUACU-UACC---------AGUAUAC--AGCCAACCACAUAUUAUACAU-AAUGCACU-AUGUAUAUUAUGGAUAGGACACUGGCUAACAGC--UGAAGUUGGUGCAAA-ACUACAAUUUCCA--------UAC--GUGGAUAACG-AAACGUC-
URS0000D6C77C_12908/1-296 CGGGUCGCU-CCCGAG--UCAUAGUUAAGG-CAAGCUAUGA--GUGCAUG-UAUUUA-------CAUGUAUU-GCAAAUCCACAUAUUCGUUGUGUUUGCAC-CACAAC-AAUAUGAGUGGGACACUAUAAUUUA-U---AAUAAUAGUGCGAAUACUGCG--UUUUC-U-UAC-------AUGGCAU--G-AGAU----
URS0000D6AEC2_12908/1-296 AGGGUAGCA-ACCUUAAUUCUUGGUGAAGG-CAAACCACGG--GUACGUA-UUAA---------UACGUAU--AGCUAUCCACAUAUUAUUCAUGUUUGCAC-CAU-GAUAAUAUGGAUAGGGCAUUGAUG-UUAGC---AUCAUUAAUGCAAA-AUUGCG--UUUUCAU-GC--------AUGUCGC--G-AAAU----
URS0000D67C41_12908/1-305 AGGGUAGCU-CCCUAU--UCUUGGUGAAGG-UAAGCCGAGA--GUACAUACAUAUUAUGUUUCGUAUGUAUUG-UAAUGCCACAUAUUGUAGUUA-AUGCAC-UAUCUAUGGUAUGGAUGGGACACUAACGAUUA-C---AACGUUAGCGCAAAAACUGAA--UUUCC--------AAACAUGGCCCG--AGAGCA-AC-
URS0000D67B6E_12908/1-309 AGGGUAGCU-CCCUAU--UCUUGGUGAAGG-UAAACCGAGA--GUACAUA-UAUCUG-------UAUGUAU---AAUUUCCACAUGUAAGUAGAUAAUGCACUAUCUUA-UACAUGGAUGGGACACUAAUAAUUA-C---ACAGUUAGUGCAAG-ACUAAA--UUUCC-A-CA---C----AUGG-GU--U-GUAU--A-
#=GC SS_cons              <<<<_____.>>>>::..<<<<<<<_____.___>>>>>>>..<<<<<<<._____........>>>>>>>..::::::::::<<<<<<<<<<<._______..>>>>>>>>>>>::::((((<<<<<<<<______..___>>>>>>>>,,,,,<<<<---.<<<<<.<.<<...-....<<________.__>>..-.
#=GC RF                   aGGgUAGCU.cCCuAu..uCuUgGugAAGG.cAAaCcAaGa..guaCauu.uUaau........aauGuau..gaaauUCCACAUAcugucugc.AuUGCAC..gcagacagUAUGGAUgGGaCAcugguaauUagC..aAauaccagUGCAAaUAcUgcaa.uuucc.c.cg...a....acGuuauaua.Augu..c.

URS0000D6ADD5_12908/1-306 -GAAA-AGUUA-----UAGUUAGAUUCAA-GCAGGA-GGAAGUAUACAAAUGUUUGAA-CCCUCUUUUACUAAAA-UCCUGA-UACU-UCGGGUGUGUGGAUGUGCAAA-UCCAUACUAUAUUAUUUAUU---GCCA------GUAA---------UGGCUGUUAGG
URS0000D68018_12908/1-295 ------GGAAGAUAGAUAAUCAGAUUCAAAACAGUU-CCACGUA---AAUUGUUUGAACUCCUAUAUU-AUUAUAUCAGUCG-UGGC-UGACAAGGAUAGAGUCGCAAA-UCUAUUCUUAUUUAU-UAU----GGG------UUGAAAUU-------CCCUGGGGAA
URS0000D658A7_12908/1-295 ------GGAAGAUAGAUAAUCAGAUUCAAAACAGUU-CCACGUA---AAUUGUUUGAACUCCUAUAUU-AUUAUAUCAGUCG-UGGC-UGAUAAGGAUAGAGUCGCAAA-UCUAUUCUUAUUUAU-UAU----GGG------UUGAAAUU-------CCCUGGGGCA
URS0000D65CDC_12908/1-295 ------GGAAGAUAAAUAAUCAGAUUCAAAACAGUU-CCACGUA---AAUUGUUUGAACUCCUAUAUU-AUUAUAUCAGUCG-UGGC-UGAUAAGGAUAGAGUCGCAAA-UCUAUUCUUAUUUAU-UAU----GGG------UUGAAAUU-------CCCUGGGGCA
URS0000D67BD7_12908/1-295 -GGAA-GAUAG----AUAAUCAGAUUCAAAACAGUU-CCACGUA---AAUUGUUUGAACUCCUACAUUAGUAUA-ACAGUCG-UGGC-UGACAAGGAUAGAGUCGCAAA-UCUAUUCUUAUUUAU-UAU----GGG------UUGAAAUU-------CCCUGGGGAA
URS0000D6A8E5_12908/1-301 CCU-GCGAAAAGUAGAUAAUCAGAUUCAA-AUACAAUGCCAAGA---AAUUGUUUGAA-UCCCUAUACAAUUGAA-ACCAGU-CUUG-GCUGG-GAGUAGAAUCGCAAA-UCUACUCUAAUUUAC-UAU----GGG------UUGAAAAU-------CCCUGGGCCC
URS0000D693F1_12908/1-301 CCU-GCGAAAAGUAGAUAAUCAGAUUCAA-AUACAAUGCCAAGA---AAUUGUUUGAA-UCCCUAUACAAUUGAA-ACCAGU-CUUG-GCUGG-GAGUAGAAUCGCAAA-UCUACUCUAAUUUAC-UAU----GGG------UUGAAAAU-------CCCUGGGCCC
URS0000D66CCC_12908/1-290 AUG-U-AGGAA-UUUGCAGUUAGAUUAGA-CAGUAUGGGAAGUACACAUGCUGUUUAA-UCCC--ACA-AUAAAAACCCUGAGUACUUACAGGUACACUGAGGUGCAAA-UCAGUGUUUUAGCC---------GCUU------CUUUG--------GAGCUGUUGGG
URS0000D6729B_12908/1-290 AUA-U-GGAAA-UUUGCAGUUAGAUUAGA-CAGUAUGGGAAACACACAUGCUGUUUAA-UCCC--ACA-AUAAAAACCCUGAGUGUUUACAGGUACACUGAGGUGCAAA-UCAGUGUUUUAGCC---------GCUC------CUUUG--------GAGCUGUUGGG
URS0000D6B0F1_12908/1-291 --------GAA-AGAGUAGUUAGAUUUAA-ACGGCU-GGAAACACACAAAUGUUUGAA-UUCU--CACAUUGGA-AUCCUGG-UGUU-UAAGGUAUACUGAAGUGCAAA-UCAGUAUUUAUU-----------GCUCC-----CAUA--------GGAGCUGUUGGG
URS0000D6C77C_12908/1-296 GUA-A-GAAAA-CUAACAGUUAGAUUUAA-ACAGAU-GGAGAUACACAAAUGUUUGAA-UCCC--AGUAACAAAAAUCCUGG-UAUC-UCGGGUAUACAGUAGUGCAGAUACUGUAUUUUUAAU---------GCUCC-----AAUA--------GGAGUUGUUGGG
URS0000D6AEC2_12908/1-296 -GC-AAGGAAAUACAGCGAUUAGAUUCGG-ACAGGA-GGAAGUACACAAAUGUUUGAA-CCCU--UUU-AACAAA-UCCCG--UACU--UGGGGGUACGGUAGUGCAAAUACCGCACUUAUAAU-UUAAU---GCUAC-----AAUA--------GUAGCUGUUGGG
URS0000D67C41_12908/1-305 ------GGAAA-UUAGCAGUUAGAUUUAA-ACAAAU-GGAAACACACAAUUGUUUGAA-UCCU--A-U-AUUAAA-UCCUGG-UGUU-UCAGGUGUACAGAGGUGCAAA-UCUGUACUAUAUUUACUAU----GGG-------UUGAAAUU------CCCUGGGGUA
URS0000D67B6E_12908/1-309 -UG-U-GGAAAGCUAAUAGUUAGAUUUAA-ACAGGA-AGAAAUACACAAAUGUUUGAA-UCCC--AAU-AUAAAAAUCCUGG-UAUU-UCAGGUACACUGAGGUGCAAA-UCAGUGUUGGGUACUCAUCUAUACUUGGAUAU-AAAU----AUAUCCGAGCGGAAAA
#=GC SS_cons              .>>.>.>>>>>.---->>>>,,,,<<<<<.<<<___._____________>>>>>>>>.))))..:::.::::::::<<<<_.____._>>>>:<<<<<<<________.>>>>>>>::::::::.:::....<<<<......_____........>>>>:::::::
#=GC RF                   .cg.g.ggaaa.uuaacAgUuAGAUUcaA.acagau.ggAaauACACAAauguUugAA.uCCc..auu.AUaAAAauccugg.Uauu.ucagguGcacgGagguGCAAA.uCcgugCUuauuuau.UAU....Gcgc......uaaAA........gcgCUGuugga
//
