                                                                        Gene putatively regulated by attenuation in C_pneumoniae_J138

                                                                        Characteristics of the secondary structures
Terminator:    Distance from promoter:71 nt.    Distance to gene:64 nt.     Distance to run of Ts=2 nt.   Size=28 nt.     Delta G= -9.80 kcal/mol
Antiterminator:    Distance from promoter:44 nt. Size=42 nt.     Delta G=-12.00 kcal/mol
Anti-antiterminator:    Distance from promoter:30 nt.    Size=36 nt.     Delta G= -4.10 kcal/mol

                                                                        Nomenclature/Definitions
The most likely promoter is: ttgcga-tacatt. It has a score value of 65.6 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

ttgcgataattagaacagaaaccgtacattcgtggctcactttatGCCGGTGTGGCGGAATGGTAGACGCGGTAGAC
TCAAAATCTACTCTTAGCAATAAGGTGTTGGTTCGAGTCCGATCACCGGCAtaattctttct
tttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttATG

    Leu --- CPj0583 Gene: CPj0583     GI: 15836115     BI number: CPj0583     GOG: NOG07060     Description: CT466 hypothetical protein Gene: atoS     GI: 15836116     BI number: CPj0584     GOG: COG0642,COG3852,COG5002     Description: 2-component senso            CA           G  A   A        AT C  A       TA T  A       TA C  A       CG AT        TG GC       |  T       GT AT        CG       A  C TA        AT        GC GC       T  T       CG GT        CG        TA C  C       TG       |  T G  |       AT       |  C C  |       AT        TA A  |      A  C       GC GT       A  |       GC AT        CG        TG TA        TA        TG G  G       CG        GC GC        AT        TA TA        GC        Gt                         aattctttcttttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [T] COG0642 Signal transduction histidine kinase ... can be seen here [T] COG3852 Signal transduction histidine kinase, nitrogen specific ... can be seen here [T] COG5002 Signal transduction histidine kinase ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in C_pneumoniae_J138                                                                         Characteristics of the secondary structures Terminator:    Distance from promoter:71 nt.    Distance to gene:72 nt.     Distance to run of Ts=2 nt.   Size=28 nt.     Delta G= -9.80 kcal/mol Antiterminator:    Distance from promoter:36 nt. Size=42 nt.     Delta G=-12.00 kcal/mol                                                                         Nomenclature/Definitions The most likely promoter is: ttgcga-tacatt. It has a score value of 65.6 and is shown in blue Bases shared by the antitermination and termination structures are shown in red The sequences of the antiterminator and terminator structures are underlined Coding regions are in CAPS, non-coding regions are in lower case ttgcgataattagaacagaaaccgtacattcgtggctcactttatGCCGGTGTGGCGGAATGGTAGACGCGGTAGAC TCAAAATCTACTCTTAGCAATAAGGTGTTGGTTCGAGTCCGATCACCGGCAtaattctttct tttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttATG     Leu --- CPj0583 Gene: CPj0583     GI: 15836115     BI number: CPj0583     GOG: NOG07060     Description: CT466 hypothetical protein Gene: atoS     GI: 15836116     BI number: CPj0584     GOG: COG0642,COG3852,COG5002     Description: 2-component senso AC T  T CC TT AT AA AG |  C       GT AA       A  C CA        GC T  T       CG CA        TA AA       |  T GG       |  C AG        TA T  T       GC G  |       GC GG        TG CT        TG GT        GC CG        TA AG        Gt             aattctttcttttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [T] COG0642 Signal transduction histidine kinase ... can be seen here [T] COG3852 Signal transduction histidine kinase, nitrogen specific ... can be seen here [T] COG5002 Signal transduction histidine kinase ... can be seen here     ..................................................................................................................