# STOCKHOLM 1.0
#=GF ID tsr24
#=GF AC RF02577
#=GF DE S. aureus tsr24 small RNA
#=GF AU Argasinska J; 0000-0003-2678-2824
#=GF GA 50.0
#=GF NC 48.9
#=GF TC 50.3
#=GF SE Argasinska J
#=GF SS Predicted; RNAfold
#=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 26861020
#=GF RT Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL MBio. 2016;7:e01990-e01915.
#=GF WK Bacterial_small_RNA
#=GF SQ 4

AM990992.1/1016690-1016925 AAAUUAUACGACGGGACCCAACACAGAAAAUUCAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUU--UAAGUAUUUCAAAGUAAAAUUACAUGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCGAGGCUGAGACGGCACCCUAGGAAAGCGAAGC
FR714927.1/1937316-1937553 AAAUUAUAAGAAGGGACCCAACACAGAAAAUUCAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUUUAAAAGUAUUUCAAAGUAAAAUUACAUGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCAAGGCUGAGACGGCACCCUAGGAAAGCGAAGC
AFNP01000039.1/58166-57929 AAAUUAUACGAAGGGACCCAACACAGAAAAUUCAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUUUUAAAGUAUUUAAAAGUAAAAUUACAUGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCGAGGCUGAGACGGCACCCUAGGAAAGCGAAGC
CP000255.1/1429517-1429754 AAAUUAUACGAAGGGAUCCAACACAGAAAAUUUAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUUUUAAAGUAUUUCAAAGUAAAAUUACACGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCGAGGCUGAGACGGCACCCUAGGAAAGCGAAGC
#=GC SS_cons               :::[[[[[[[[,,,,,,,,,,,,,,,<<<<<<<<______>>>>>>>><<<<<<-<<<-<<___>>->>>>>>>>>,,,,,,,,,,,,,,,((((((,,,<<<____>>><<<<____>>>>,<<<<<<<<<<<-----<<<<-<<<<-<<-<<--<<<<<_________>>>>>-->>->>->>>>>>>>------->>
#=GC RF                    AAAuuauacgaaGGGAcCCAACACAGaaaauucaUUUUAUugaauuuuaCacuuAuGcGCaAGUuGGgCaaaguGuCUUAUUUUUUuaAAGuacuucAAAGuaAAAUuaCacGuUAAUaCguAGuauuaauGGCGAGACuCCuGaGGGAGCAGuGCCaGcCGAAGACCgAGgCuGAGaCGGCACCCuaGGaAAGCGAAGC

AM990992.1/1016690-1016925 CAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
FR714927.1/1937316-1937553 CAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
AFNP01000039.1/58166-57929 CAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
CP000255.1/1429517-1429754 CAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
#=GC SS_cons               >>>>->>>>>))))))]]]]]]]]::::::::::::::
#=GC RF                    CauuCaauaCgaaguaucguauaaAUAGAGAACAGCAG
//
