# STOCKHOLM 1.0

#=GF AC   RF00101
#=GF ID   SraC_RyeA
#=GF DE   SraC/RyeA RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   37.00
#=GF TC   37.20
#=GF NC   36.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00105
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [2]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF CC   This RNA was discovered in E. coli during a large scale screens [1-2]. The
#=GF CC   function of this RNA is unknown. This RNA overlaps RFAM:RF00111 on the
#=GF CC   opposite strand suggesting that the two may act in a concerted manner.
#=GF WK   SraC/RyeA_RNA
#=GF SQ   13


AL627272.1/127686-127830     AAUUAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
CP000653.1/2601613-2601758   AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAUAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAACUAC-GCCUGACACUCUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUCC
AE017042.1/1756200-1756347   AAUUAAAAAAAGACCGAAUACGAUUCCUGAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGUAUUAAU----GUAGGCUUAUU-CAGCCGCACUUCUUAAGCGUAGCCGAGUACCGACAUUUCGCCAACCUU
CP000034.1/1046100-1046244   AAUGAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
CP000647.1/2580976-2581120   AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAGU-C-GCCUUGCACUAUAAGAAUAGUUUAACG-CGUCAGCUUUUCCAGUCC
AM286415.1/1991675-1991530   AAUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCAUACUCUUUAAGAGUAGUCGAGGU-CAUGUGUUUCGCCAACUU
CU928145.2/2074283-2074427   AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
CP000970.1/1336993-1336849   AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGAUUUUCCAGUUU
AM933172.1/1226335-1226191   AAAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
AALD02000029.1/37435-37580   ACUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCGUACUACUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU
AALC02000009.1/70496-70641   AGAUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUAUUUAGCCAACUU
AALF02000003.1/121616-121765 AAUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGACAGAGCCGUGCGCUAAAAGUUGGCAUUAAUUAACGUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUAGCCAACUU
AALE02000013.1/38-183        AGUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAGGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU
#=GC SS_cons                 :::::::::::<<<<<<<<<<_______>.>>>>>>>>>,,,,,,,<<<<<<<<______>>>>>>>>,,<<_________>>,,,,,,....,,,<<<_____._.>>>::::::::::::::::::::::::.::::::::::::::::::
#=GC RF                      AauUAAAAAaAGaCCGaauacGAUUCCUg.uauuCGGuCuAGGGAAauGGCuCuUGGGAgaGaGCCguGCGCUAAAAGUUGGCAUUAAu....GuAGGCUuAuU.c.GCCuuaCucuUUAAGaaUAGuuGAguA.CgucaguUUuuCcAauUU
//