                                                                        Gene putatively regulated by attenuation in C_pneumoniae_TW_183

                                                                        Characteristics of the secondary structures
Terminator:    Distance from promoter:46 nt.    Distance to gene:62 nt.     Distance to run of Ts=2 nt.   Size=31 nt.     Delta G=-13.30 kcal/mol
Antiterminator:    Distance from promoter:32 nt. Size=29 nt.     Delta G=-11.50 kcal/mol
Anti-antiterminator:   Size=80 nt.     Delta G= -6.61 kcal/mol

                                                                        Nomenclature/Definitions
The most likely promoter is: TTTCTA-taaaat. It has a score value of 64.26 and is shown in blue
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

TTTCTACGCTCTGAtcttctcttataaaattaataaaccccttggtatcaatcatttgggatagccccttagaatcttgactctaagggc
ttctccttagagatcgatctttgttgttagaatttttccctagattctaatacagtagatcagaaaaacaaaagtaacccacgtcctATG

    cpdA Gene: cpdA     GI: 33242259     BI number: CpB0928     GOG: COG1409     Description: 3,5'-cyclic-nucleotide phosphodiesteras a  a ta gt gc ta |  t |  t t  t cg cg cg c  a a  t a  | a  | t  | a  | a  | t  | t  | a  | a  | a  | a  | t  | a  | t  | t  | c  | t  | c  | t  | t  | c  | t  | A  | G  | T  | C  | Ta                  tt Cg        tt       c  c Gc       c  g       gt |  c      t  a       gc |  c      a  c       gc |  c       at        at C  t       gc        at At        at        ta Ta        ta        cg Cg        ta        ta T  |      c  |       cg Ta        cg       |  a Ta        cg        at At        cg        gc Gc        gc        tg At        at        ta                         tctttgttgttagaatttttccctagattctaatacagtagatcagaaaaacaaaagtaacccacgtcctATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [R] COG1409 Predicted phosphohydrolases ... can be seen here     ..................................................................................................................