Gene putatively regulated by attenuation in A_tumefaciens_C58_UWash_linear

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:198 nt.     Distance to run of Ts=0 nt.   Size=17 nt.     Delta G= -7.40 kcal/mol
Antiterminator: Size=56 nt.     Delta G=-14.00 kcal/mol
Anti-antiterminator:   Size=35 nt.     Delta G= -5.40 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

CGTTCTAAAGAAATCAGGTTGATGAGCTGAATGCTTGTTGTTTTCCAAGGGCTTTTAG
CTTTTGGGGTTTGATTTTGTGACTGCATTGAGCGGTCTGTTTTTTGACAATTGAATAT
GAGAAGAAAGAGAAACGTGGGCGGCGAAGCTTGCGGGACCTGGAGAGATTTGGGTCCT
AGTGAATAGACTTTGACGGTCACgttttaatgagacaacaccaatttcgcgagcagagatgtttgttgagattgatgtgagtt
ctcgtcgattcagaataacgtgacaatagtcaatgattgaattCTC

    SSU --- 16S --- rRNA_v2 --- tRNA --- Ile_v2 --- tRNA --- Ala_v3


Gene: SSU-16S-rRNA_v2     GI: Atu4180     BI number: Atu4180     GOG: -------     Description: SSU 16S ribosomal RNA
Gene: tRNA-Ile_v2     GI: Atu4181     BI number: Atu4181     GOG: -------     Description: tRNA-Ile
Gene: tRNA-Ala_v3     GI: Atu4182     BI number: Atu4182     GOG: -------     Description: tRNA-Al


            T
          T  T
          T  A
           CG
           GC
           GT
           GT
           AT
           AT
           CG
           CG
           TG
           TG
          T  T
 aa       T  T
g  t       GT
t  t       TG
t  C       TA
 aT        GT
 gC       |  T
 tA       |  T
 aT       |  T
a  G      |  G
c  C      |  T        T
t  |      |  G      T  G
 gT       |  A      A  A
 aT       T  C       CG
 tG       T  T       GC
 aT        CG        TG
 aT        GC        CG
 cG        TA        AT
 aT        AT        GC
                        TGTTTTTTGACAATTGAATATGAGAAGAAAGAGAAACGTGGGCGGCGAAGCTTGCGGGACCTGGAGAGATTTGGGTCCTAGTGAATAGACTTTGACGGTCACgttttaatgagacaacaccaatttcgcgagcagagatgtttgttgagattgatgtgagttctcgtcgattcagaataacgtgacaatagtcaatgattgaattCTC
    ..................................................................................................................