# STOCKHOLM 1.0 #=GF ID ffh #=GF AC RF01793 #=GF DE ffh sRNA #=GF AU Meyer MM; 0000-0001-7014-9271 #=GF GA 35.0 #=GF NC 34.9 #=GF TC 35.0 #=GF SE Published; PMID:19531245 #=GF SS Published; PMID:19531245 #=GF TP Gene; sRNA; #=GF BM cmbuild -F CM SEED #=GF CB cmcalibrate --mpi CM #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 29.24 -Z 2958934 CM SEQDB #=GF DR SO; 0000370; small_regulatory_ncRNA; #=GF RN [1] #=GF RM 19531245 #=GF RT Identification of candidate structured RNAs in the marine organism #=GF RT 'Candidatus Pelagibacter ubique'. #=GF RA Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, #=GF RA Breaker RR #=GF RL BMC Genomics. 2009;10:268. #=GF WK Pelagibacter_ubique #=GF ** seedtax: Bacteria; unclassified sequences #=GF SQ 89 ABEF01041528.1/252-304 -AAA-CAAA---GGUAUCG-ACACUAGU-CAGCGAGGGUUCGCCCACUAGUGC-GAUU-UUU ABID01000001.1/620465-620516 UGACGUCG-----GGAUCG-CCCCCAGU-CAGCGCGU-UGCGCCCACUGGGGC-AUUU-GUG CP000830.1/337335-337284 CUGUGCAG-----GGAUCG-CCACCCGU-CAGCGCGU-UGCGCCCACGGGUGC-CUUU-CCG CP000264.1/722337-722286 CGUCCGCA-----GGAUCG-CCCCCCGU-CAGCGAGU-UUCGCCCACGGGGGC-AAAU-CUC ABXE01000005.1/474503-474554 UUGCAUGA-----GGAUCG-CCACCAGU-CAGCGCGU-CGCGCCCACUGGUGC-GUUU-CUC AATR01000007.1/128120-128172 CGGUCUCA-----GGAUCG-ACAUCAGU-CAGCGAGU-UUCGCCCACUGGUGUUAAUU-GCG CP000577.1/2858994-2858943 CACGACCG-----GGAUCG-CCACCCAU-CAGCGCGA-UGCGCCCAUGGGUGC-CGUU-GUG ABVS01000001.1/307524-307576 AAACAAAG-----AGAUCG-ACACUAGU-CAGCGAGGCUUCGCCCACUAGUGC-GAUU-ACU ABSK01000020.1/158486-158537 CCACGCAA-----GGAUCG-CCCCCAGU-CAGCGCGU-UGCGCCCACUGGGGU-UAAA-CUG AAMO01000005.1/155351-155300 CGUUGCGG-----GGAUCG-CCACCAGU-CAGCGCGU-CGCGCCCACUGGUGC-AAUC-GUC AAOT01000022.1/32279-32331 GCCCGUCG-----GGAUCG-CCCCCCGU-CAGCGAGCGUUCGCCCACGGGGGC-GUUU-GCC CP000084.1/260256-260205 AAACAAAG-----AGAUCA-ACACUAGU-CAGCGAUA-UUCGCCCACUAGUGC-GAAA-CUG ABSH01000046.1/28800-28749 UAGACUGA-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-UCUA-CUG ABCL01000001.1/633361-633412 CUGUGUCG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUUU-AUC ACOA01000003.1/1141569-1141620 AUGUUCAG-----GGAUCG-CCCCCCAC-CAGCGAGU-UUCGCCCGUGGGGGC-AUUU-GUG CP000661.1/172455-172506 CUUGUCCG-----GGAUCG-CCACCCAU-CAGCGCGA-UGCGCCCAUGGGUGC-CGUU-GUU AATQ01000012.1/82408-82357 UUUGCCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-CAUU-CUG CP000490.1/1013005-1013056 CUUGCCGG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUUA-CUG AAMS01000004.1/308726-308675 CAUUCAGG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUUC-CUG AAMT01000001.1/87588-87537 UUAUGCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GCUA-CUG ABCR01000008.1/127115-127064 UUUGGCCG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGA-GAUU-GGC AAYA01000021.1/1331-1382 AUGGCCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-AUUU-CCG ABXS01000046.1/690533-690482 GCAGCCAA-----AGAUCG-ACCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AUUU-GUG AALY01000001.1/1810888-1810837 CCUGCCCG-----GGAUCG-CCCCCCAC-CAGCGCGU-UGCGCCCGUGGGGGC-AAUU-GUG ACNW01000095.1/91055-91106 UAUGCCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-UGUU-UCG ACCW01000020.1/70965-70914 UCGUUCAG-----GGAUCG-CCCCCCAC-CAGCGAGU-UUCGCCCGUGGGGGC-AAUG-CCA CP000362.1/1269963-1269912 UGCAACCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-AAAA-CCA AAXZ01000001.1/683078-683027 GAUGCUUG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGGGGC-GUUU-GUG AAYB01000002.1/428943-428892 AUAUCAGG-----GGAUCG-CCCUCCGU-CAGCGCGU-CGCGCCCACGGGGGC-GCUA-CUG AALV01000001.1/423960-424011 GCGGCCAG-----AGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AUUU-GCG AANB01000002.1/544189-544138 CUUGUCGG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAUU-GCG CP000377.1/2739930-2739981 UUUGCCAG-----GGAUCG-CCCUCCAC-CAGCGCGU-UGCGCCCGUGGGGGC-AAAC-CUU ABIE01000022.1/29479-29428 AUUGCCGG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGGGGU-GAUU-GCG ABXL01000036.1/20582-20633 GAUCCCAG-----AGGUCA-ACACCCGA-CAGCGCGA-UGCGCCCUCGGGUGA-UUUU-UUG CP000628.1/3527839-3527890 GAUCCCGG-----AGGUCA-ACACCCGA-CAGCGCGU-UGCGCCCUCGGGUGC-UUUU-UGG ABOG01005133.1/88-35 GAAUUCCA-----GGAUCG-CCCCCCGUCCAGCGAGGUUUCGCUCACGGGGGU-AUUG-GUG ABIA02000001.1/8978-8927 GAUCCCGG-----AGGUCA-CCACCCGA-CAGCGCGA-UGCGCCCUCGGGUGU-UGUU-UGG AP009384.1/4516671-4516722 GGGUCCGG-----AGGUCA-CCGCCCGA-CAGCGCGU-UGCGCCCUCGGGCGC-GUUU-CUC AL591688.1/3522329-3522379 GAGCCCGG-----AGGUCA-ACACCCGA-CAGCGCGU-UGCGCCCUCGGGUG--GUUU-UUG CP000633.1/3538560-3538610 GUUCCCGG-----AGGUCA-ACACCCGA-CAGCGCGA-UGCGCCCUCGGGUG--AUUU-UUG CP000494.1/368234-368183 GAGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCUA-UGCGCCCUCGGGCGC-AAAU-GUG CP000250.1/397403-397351 GAGACCGG-----AGGUCA-ACGCCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-CAUAAGUG CP000781.1/1675762-1675712 GGGUCCGG-----AGGUCA-CCGCCCGA-CAGCGCGU-UGCGCCCUCGGGCGC-GAU--CUG AAFX01130413.1/507-455 GCGCCCAA-----GGGUGC-ACGCCGGU-CAGCGAGGUUUCGCCCACCGGCGU-CUUU-GUC CP001096.1/263306-263254 GAGGCCGG-----AGGUCA-ACGUCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-AAUAAGUG CP000758.1/1121355-1121406 GAUCCCGG-----AGGUCC-ACAUCCGA-CAGCGCGA-UGCGCCCUCGGGUGC-UGUA-UCG CP000283.1/583300-583249 GAGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-GAAC-GUG ACCU01000015.1/1002967-1002917 UUCCCGGA-----GGUUC--ACAUCCGA-CAGCGCGA-UGCGCCCUCGGGUGU-CAAA-CUG CP001488.1/1778730-1778679 GAUCCCGG-----AGGUCC-ACACCCGA-CAGCGCGA-UGCGCCCUCGGGUGC-CGUG-ACC AACY023196554.1/144-92 CAUGUUCA-----GGAUCG-CCCCCCGU-CAGCGAGGUUUCGCCCACGGGGUC-AAUU-UUG AACY023876466.1/1379-1328 -----UAGCAGUUGGAUCG-CCCCCCGU-CAGCGAGU-UUCGCCCACGGGGGU-AAUU-ACG AACY020558092.1/912-963 UAAC----AG-UUGGAUCG-CCCCCCGU-CAGCGAGU-UUCGCCCACGGGGGUAAGU--GGG AACY020314903.1/269-217 GGUCCAUA-----AGAUCG-CCGUUCGU-CAACGAGGCUUCGUACACGAACGC-AAUA-CUU AACY020277128.1/1252-1200 UUCAAAAG-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGAUGC-UUUU-GUU AACY023061866.1/133-185 UUCACAAU-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGAUGU-UUUU-GUU EU016673.1/15743-15714 ---------------------CACUAGU-CAGCGAGGGUUCGCCCACUAGUG---------- AACY023081810.1/148-96 UUCACAAU-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGGUGC-UUUU-GUU AACY020537384.1/5298-5349 GAUCGCGG-----GGAUC-ACCACCGGU-CGGCGAGU-UUCGCCCACCGGUG--CAUUUUGC AACY021910620.1/877-825 UUCACAGU-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGAUGC-UUUU-GUU AACY022176703.1/377-428 CCCUCUUU-----GGAUCU-ACAUCCGU-CAGCGUUG-UACGCCCGCGGGUGC-CAUU-ACG AAFX01131867.1/488-457 ------------------A-CCGCCCGA-CAGCGCAA-UGCGCCCUCGGGCGU--------- AACY023681284.1/528-562 -----------------CG-ACACUAGU-CAGCGAGGCUUCGCCCACUAGUGC-G------- AACY020533898.1/2363-2414 UUGGGCAG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUCU-GUG AACY020307803.1/379-431 AAGUGCCG-----GGAUCGCCCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-GCUU-GUG AACY021683092.1/259-208 UUGCCCAA-----GGAUCG-CCACCCGU-CAGCGCGU-UGCGCCCACGGGUGC-GUUU-UUG AACY020400269.1/2767-2715 -GAA-CAAA---GAGAUCG-ACACUAGU-CAGCGAGGGUUCGCCCACUAGUGC-GAUUACU- AACY020080831.1/570-622 GGUCCAAA-----AGAUCG-CCGUUCGU-CAACGAGGCUUCGUACACGAACGC-GAUA-CUU AAYC01000003.1/36039-36090 CCUGUCAG-----GGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAUU-CUG CP000031.1/3449415-3449466 UUGUCCGG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGAGGC-GAUU-GUG ABXM01000014.1/117294-117243 CGUGCCAG-----GGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAUU-GCG ABXF01000044.1/222593-222644 CGUGCCAG-----GGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAAC-UCG ACNZ01000021.1/2003-2054 UGGGUCGG-----GGAUCG-CCCUCCAC-CAGCGCGU-UGCGCCCGUGGGGGC-AAAC-CUU CP000390.1/3614033-3613982 GAUCCCGG-----AGGUCA-ACACCCGG-CAGCGCAA-UGCGCCCCCGGGUGC-UUUU-CGG AAUW01000013.1/152797-152746 GAUCCCGG-----AGGUUA-CCAUCCGA-CAGCGCGU-UGCGCCCUCGGGUGU-CAAA-CUG CP001029.1/673842-673894 GAGGCCGG-----AGGUCA-ACGUCCGA-CAGCGCGUCUGCGCCCUCGGGCGC-CCUU-GUC CP000524.1/76871-76922 GAUCCCAG-----AGGUCA-ACACCCGA-CGACGCGU-UGCGUUCUCGGGUGU-UAUU-UUG CP000463.1/366625-366676 GAGACCGG-----AGGUUA-ACGCCCGA-CAGCGCUG-UGCGCCCUCGGGCGC-AAAA-UUG BA000012.4/3476818-3476869 GAUCCUGG-----AGGCCA-ACACCCGG-CAGCGCAA-UGCGCCCCCGGGUGC-UUUU-UGG ABPX01008569.1/496-547 AGGAGACA-----GAAUGA-CCAUCCGC-CAGCGCGU-UGCGCCCGCGGGUGC-UGCU-UUG CP000115.1/3019357-3019408 GGGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCUG-UGCGCCCUCGGGCGC-AAAC-GUG CP000738.1/3241936-3241986 GAGCCAGG-----AGGUCA-ACAUCCGA-CAGCGCGU-GGCGCCCUCGGGUG--GUUU-UUG CP001196.1/260758-260809 GACGCCGG-----AGGCCA-ACGCCCGA-CAGCGCUG-UGCGCCCUCGGGCGU-AAAC-GUG CP001001.1/3845723-3845671 GAGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCGUCCGCGCCCUCGGGCGC-GAUG-GGC AM260525.1/2496302-2496251 GAUCUCAG-----AGGUCA-ACAUUCGA-CGGCGCGA-UGCGUUCUCGGGUGC-UAUU-UUG BX897700.1/1505050-1504999 GAUCUCAG-----AGGUCA-ACAUCCGA-CGGCGCGA-UGCGUUCUCGGAUGC-CACU-UUA AATP01000001.1/786255-786204 CCGCCCGG-----AGGUCA-CCAUCCGC-CAGCGAGU-UUCGCCCGCGGAUGG-CGUU-UUG BX897699.1/1849078-1849027 GAUCUCAG-----AGGUCA-ACAUCCGA-CGGCGCGG-UGCGUUCUCGGAUGC-UGCU-UUG CP001349.1/2975644-2975695 GAGGCUGG-----AGGCCA-ACGCCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-GUCC-GGC CP001016.1/3804515-3804563 AAACCCCG-----G---CC-ACGCCCGG-CAGCGCGU-UGCGCCCCCGGGCGC-GUUU-UGC #=GC SS_cons ::::::::.....::::::.:<<<<<<<.--<<<<__._>>>>-->>>>>>>:.::::.::: #=GC RF gaucCCgG.....GGAUCG.CCaCCCGu.CAGCGCGu.UGCGCCCaCGGGuGC.aaUU.gUG //