                                                                        Gene putatively regulated by attenuation in A_aeolicus

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:187 nt.     Distance to run of Ts=3 nt.   Size=22 nt.     Delta G= -6.30 kcal/mol
Antiterminator: Size=29 nt.     Delta G= -3.36 kcal/mol
Anti-antiterminator:   Size=21 nt.     Delta G= -3.50 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

ACGTTCTCTCTATTATGAGAAGTCTGCTTTCTTCCCTTTTCTCCTTTCCTTCTTTCTT
ACCTTCTATAAAACCGCGTGAGAACTCCTTCAGGATTTCTTCTACTTTTTTTCTCTCT
TCCGGCTTTAATACTTCCGGGTTTTCAAGGATTATCAAGCTTCCTTTGAATATATTGT
GGGAGAGTTTTTCTTTCAATTCTTTAAGTAATTTATCTATGTTTCCTTTTTCCTTTAT
CTTTATCTGGATTACGGGAAGTGTTTTTCCCTTTATCTCTATCACcttaactattattataaggaag
tATG

    aq_880 Gene: aq_880     GI: 15606219     BI number: aq_880     GOG: COG1458     Description: hypothetical protei             A           T  A           A  A           T  A TG       C  C       TC A  T      T  C      T  A t  T      T  G       CG gC       C  C       CG aT        CG        TA aT        AT       C  T |  A       TG        AT gC        TA        AT gC        CG        GC aT        TA        AT aT        TA        GT                         CTACTTTTTTTCTCTCTTCCGGCTTTAATACTTCCGGGTTTTCAAGGATTATCAAGCTTCCTTTGAATATATTGTGGGAGAGTTTTTCTTTCAATTCTTTAAGTAATTTATCTATGTTTCCTTTTTCCTTTATCTTTATCTGGATTACGGGAAGTGTTTTTCCCTTTATCTCTATCACcttaactattattataaggaagtATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [R] COG1458 Predicted DNA-binding protein containing PIN domain ... can be seen here     ..................................................................................................................