# 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
//
