                                                                        Gene putatively regulated by attenuation in C_caviae

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:99 nt.     Distance to run of Ts=0 nt.   Size=22 nt.     Delta G=-13.60 kcal/mol
Antiterminator: Size=48 nt.     Delta G= -6.15 kcal/mol
Anti-antiterminator:   Size=45 nt.     Delta G=-10.30 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

ctaatttttgcgctccagaagctgccgcaatattaagatctccacaatcttaatattgctggacagtttggtacgagtacctcatctggaacgacagcga
tgcactttcttgcatttaccggctctttttccctctcctcttatttttaagttttttcgcaaggtgccgccaccttgcgtttttttttgtttttttctct
tttaaattcttcttaagttcttttttttgaattaattattttttattttaaaattaaaacataactaatgggtattttttaaaaactctgagaataaatt
ATG

    CCA00451 --- CCA00452 Gene: CCA00451     GI: 29840213     BI number: CCA00451     GOG: NOG04986     Description: conserved hypothetical protein Gene: CCA00452     GI: 29840214     BI number: CCA00452     GOG: NOG07053     Description: conserved hypothetical protei tt        tt t  c      t  t c  t       at at        ta cg        ta gc        cg ta       t  t at       c  t gt       c  t |  t      t  t |  a      c  t |  c      t  t |  c      c  c |  g      c  g cg       c  c       cg gc       t  |      c  c at       t  |       gc c  c       ta        ta at        ta        gc gt        tg        gc c  t       cg        at at       t  t       at at        cg        cg gc        gc        gc gc        gc        cg                         tttttttttgtttttttctcttttaaattcttcttaagttcttttttttgaattaattattttttattttaaaattaaaacataactaatgggtattttttaaaaactctgagaataaattATG     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in C_caviae                                                                         Characteristics of the secondary structures Terminator:    Distance to gene:106 nt.     Distance to run of Ts=0 nt.   Size=22 nt.     Delta G=-13.60 kcal/mol Antiterminator: Size=48 nt.     Delta G= -6.15 kcal/mol Anti-antiterminator:   Size=45 nt.     Delta G=-10.30 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 ctaatttttgcgctccagaagctgccgcaatattaagatctccacaatcttaatattgctggacagtttggtacgagtacctcatctggaacgacagcga tgcactttcttgcatttaccggctctttttccctctcctcttatttttaagttttttcgcaaggtgccgccaccttgcgtttttttttgtttttttctct tttaaattcttcttaagttcttttttttgaattaattattttttattttaaaattaaaacataactaatgggtattttttaaaaactctgagaataaatt ATG     CCA00451 --- CCA00452 Gene: CCA00451     GI: 29840213     BI number: CCA00451     GOG: NOG04986     Description: conserved hypothetical protein Gene: CCA00452     GI: 29840214     BI number: CCA00452     GOG: NOG07053     Description: conserved hypothetical protei tt        tt t  c      t  t c  t       at at        ta cg        ta gc        cg ta       t  t at       c  t gt       c  t |  t      t  t |  a      c  t |  c      t  t |  c      c  c |  g      c  g cg       c  c       cg gc       t  |      c  c at       t  |       gc c  c       ta        ta at        ta        gc gt        tg        gc c  t       cg        at at       t  t       at at        cg        cg gc        gc        gc gc        gc        cg                         tttttttttgtttttttctcttttaaattcttcttaagttcttttttttgaattaattattttttattttaaaattaaaacataactaatgggtattttttaaaaactctgagaataaattATG     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in C_caviae                                                                         Characteristics of the secondary structures Terminator:    Distance to gene:113 nt.     Distance to run of Ts=0 nt.   Size=22 nt.     Delta G=-13.60 kcal/mol Antiterminator: Size=48 nt.     Delta G= -6.15 kcal/mol Anti-antiterminator:   Size=45 nt.     Delta G=-10.30 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 ctaatttttgcgctccagaagctgccgcaatattaagatctccacaatcttaatattgctggacagtttggtacgagtacctcatctggaacgacagcga tgcactttcttgcatttaccggctctttttccctctcctcttatttttaagttttttcgcaaggtgccgccaccttgcgtttttttttgtttttttctct tttaaattcttcttaagttcttttttttgaattaattattttttattttaaaattaaaacataactaatgggtattttttaaaaactctgagaataaatt ATG     CCA00451 --- CCA00452 Gene: CCA00451     GI: 29840213     BI number: CCA00451     GOG: NOG04986     Description: conserved hypothetical protein Gene: CCA00452     GI: 29840214     BI number: CCA00452     GOG: NOG07053     Description: conserved hypothetical protei tt        tt t  c      t  t c  t       at at        ta cg        ta gc        cg ta       t  t at       c  t gt       c  t |  t      t  t |  a      c  t |  c      t  t |  c      c  c |  g      c  g cg       c  c       cg gc       t  |      c  c at       t  |       gc c  c       ta        ta at        ta        gc gt        tg        gc c  t       cg        at at       t  t       at at        cg        cg gc        gc        gc gc        gc        cg                         tttttttttgtttttttctcttttaaattcttcttaagttcttttttttgaattaattattttttattttaaaattaaaacataactaatgggtattttttaaaaactctgagaataaattATG     ..................................................................................................................