                                                                        Gene putatively regulated by attenuation in C_pneumoniae_TW_183

                                                                        Characteristics of the secondary structures
Terminator:    Distance from promoter:71 nt.    Distance to gene:82 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
TCAAAATCTACTCTTAGCAATAAGGTGTTGGTTCGAGTCCGATCACCGGCATaattctttc
ttttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttatgaatgaaagaaccctcTTG

    CpB0607 --- atoS Gene: CpB0607     GI: 33241938     BI number: CpB0607     GOG: NOG07060     Description: hypothetical protein Gene: atoS     GI: 33241939     BI number: CpB0608     GOG: COG0642,COG2202     Description: Ato            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                         aattctttcttttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttatgaatgaaagaaccctcTTG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [T] COG0642 Signal transduction histidine kinase ... can be seen here [T] COG2202 FOG: PAS/PAC domain ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in C_pneumoniae_TW_183                                                                         Characteristics of the secondary structures Terminator:    Distance from promoter:71 nt.    Distance to gene:90 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 TCAAAATCTACTCTTAGCAATAAGGTGTTGGTTCGAGTCCGATCACCGGCATaattctttc ttttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttatgaatgaaagaaccctcTTG     CpB0607 --- atoS Gene: CpB0607     GI: 33241938     BI number: CpB0607     GOG: NOG07060     Description: hypothetical protein Gene: atoS     GI: 33241939     BI number: CpB0608     GOG: COG0642,COG2202     Description: Ato 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             aattctttcttttttcaggttgccaataaattgttttgtcgtttttcttagggaaaaccaaagtaacaccccgatttcttatgaatgaaagaaccctcTTG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [T] COG0642 Signal transduction histidine kinase ... can be seen here [T] COG2202 FOG: PAS/PAC domain ... can be seen here     ..................................................................................................................