                                                                        Gene putatively regulated by attenuation in A_aeolicus

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:176 nt.     Distance to run of Ts=2 nt.   Size=25 nt.     Delta G= -7.10 kcal/mol
Antiterminator: Size=42 nt.     Delta G= -8.82 kcal/mol
Anti-antiterminator:   Size=48 nt.     Delta G=-16.70 kcal/mol

                                                                        Nomenclature/Definitions
Bases shared by the antitermination and termination structures are shown in red
Bases shared by the anti-antitermination and antitermination structures are shown in green
The sequences of the anti-antiterminator, antiterminator and terminator structures are underlined
Coding regions are in CAPS, non-coding regions are in lower case

TGTATCCCTTGTTTACGAGTTTAGCTATGTAGGAGTTTGCGGAGTGGTAGGGAACTCC
GCACATGGGTATCCTTTCCTTTCCCTTTCCCGCGGGTCTTGAGGTGAGAACAAGTCCC
AGTTCTTTAGAGCCTATGTAAGCGTCTTCGTAAAAGAGCTCGTAAAAGTCTCCGAGTC
TGAAGAGAAGCAAACAGTCGGGGTACTGATTTTTGAAGTAGTGGTATTGTGAGAGCAT
GGGAGTGAGCTCTTTCTCAGATTTCTCCATaagaaagaaaatttaaaccatttcgtaaaataatccttATG

    ileS --- aq_303 --- aq_302 Gene: ileS     GI: 15605834     BI number: aq_305     GOG: COG0060     Description: isoleucyl-tRNA synthetase Gene: aq_303     GI: 15605833     BI number: aq_303     GOG: COG1226     Description: hypothetical protein Gene: aq_302     GI: 15605832     BI number: aq_302     GOG: NOG42182     Description: putative protei AG T  G G  G G  A TA GC         T AT       T  T GC       C  C GC       C  C CG       T  T GC       A  T T  |      T  T T  |       GC T  |       GC G  |       GC A  |      |  T        G G  |      |  T      T  A G  |      T  T      G  G A  |      A  C      G  A TA       C  C      A  A GC       A  C       GC TA        CG        TA AT        GC        TA TG        CG        CG CG        CG       T  T G  G      T  |       GC AT        CG        GC TA        AT        GC                         AGTTCTTTAGAGCCTATGTAAGCGTCTTCGTAAAAGAGCTCGTAAAAGTCTCCGAGTCTGAAGAGAAGCAAACAGTCGGGGTACTGATTTTTGAAGTAGTGGTATTGTGAGAGCATGGGAGTGAGCTCTTTCTCAGATTTCTCCATaagaaagaaaatttaaaccatttcgtaaaataatccttATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [J] COG0060 Isoleucyl-tRNA synthetase ... can be seen here [P] COG1226 Kef-type K+ transport systems, predicted NAD-binding component ... can be seen here     ..................................................................................................................