                                                                        Gene putatively regulated by attenuation in B_aphidicola_Sg

                                                                        Characteristics of the secondary structures
Terminator:    Distance from promoter:142 nt.    Distance to gene:108 nt.     Distance to run of Ts=3 nt.   Size=23 nt.     Delta G= -6.50 kcal/mol
Antiterminator:    Distance from promoter:115 nt. Size=41 nt.     Delta G= -8.20 kcal/mol
Anti-antiterminator:    Distance from promoter:77 nt.    Size=57 nt.     Delta G= -3.21 kcal/mol

                                                                        Nomenclature/Definitions
The most likely promoter is: TTTATT-TAAAAT. It has a score value of 66.27 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

TTTATTCATCCTTATTTATTTATATCTAAAATTTTATCCTATGAACCATTTGATTTTT
TTCCTACTTTTTTTGTTGCATTTATTAAAAAAACTAACTCAATTGTATTAAAAAGCGT
TAATGGTAATGTAAAATGCTACATATCAACGATGTTTGTTGGTATTAATTTGTTTTTT
ATTTTAGTTTTATGTTCTTTTTTATCATAGaaatgttttttattagttgtttttaaatttttacatcctttttttgat
tatattaatataataaataataggaatatacgtctaATG

    nuoM --- nuoN Gene: nuoM     GI: 21672448     BI number: BUsg158     GOG: COG1008     Description: NADH dehydrogenase I chain M Gene: nuoN     GI: 21672449     BI number: BUsg159     GOG: COG1007     Description: NADH dehydrogenase I chain AA C  T T  T CG AT |  A |  T |  T A  A T  A C  A       AT A  A      A  G A  A      A  C A  G       AT A  C       TA A  G       GC AT        TA AT       A  | TA        AT TA        TA         G AT        GT       T  T TG        GC        AT |  G       TA        GT |  T      A  A       CG TA       A  C       AT TA        TG        AT AT        TA        CG CG        GT        TG GT        CG        AT TA        GT        TA TA        AT        AT                         TAATTTGTTTTTTATTTTAGTTTTATGTTCTTTTTTATCATAGaaatgttttttattagttgtttttaaatttttacatcctttttttgattatattaatataataaataataggaatatacgtctaATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [C] COG1008 NADH:ubiquinone oxidoreductase subunit 4 (chain M) ... can be seen here [C] COG1007 NADH:ubiquinone oxidoreductase subunit 2 (chain N) ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in B_aphidicola_Sg                                                                         Characteristics of the secondary structures Terminator:    Distance from promoter:142 nt.    Distance to gene:115 nt.     Distance to run of Ts=3 nt.   Size=23 nt.     Delta G= -6.50 kcal/mol Antiterminator:    Distance from promoter:106 nt. Size=41 nt.     Delta G= -8.20 kcal/mol                                                                         Nomenclature/Definitions The most likely promoter is: TTTATT-TAAAAT. It has a score value of 66.27 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 TTTATTCATCCTTATTTATTTATATCTAAAATTTTATCCTATGAACCATTTGATTTTT TTCCTACTTTTTTTGTTGCATTTATTAAAAAAACTAACTCAATTGTATTAAAAAGCGT TAATGGTAATGTAAAATGCTACATATCAACGATGTTTGTTGGTATTAATTTGTTTTTT ATTTTAGTTTTATGTTCTTTTTTATCATAGaaatgttttttattagttgtttttaaatttttacatcctttttttgat tatattaatataataaataataggaatatacgtctaATG     nuoM --- nuoN Gene: nuoM     GI: 21672448     BI number: BUsg158     GOG: COG1008     Description: NADH dehydrogenase I chain M Gene: nuoN     GI: 21672449     BI number: BUsg159     GOG: COG1007     Description: NADH dehydrogenase I chain TA G  A G  T TG AT AA TA T  | GA CA         G GT       T  T AG        AT AC        GT A  T       CG A  A       AT AC        AT TA        CG TT        TG AA        AT TT        TA GC        AT             TAATTTGTTTTTTATTTTAGTTTTATGTTCTTTTTTATCATAGaaatgttttttattagttgtttttaaatttttacatcctttttttgattatattaatataataaataataggaatatacgtctaATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [C] COG1008 NADH:ubiquinone oxidoreductase subunit 4 (chain M) ... can be seen here [C] COG1007 NADH:ubiquinone oxidoreductase subunit 2 (chain N) ... can be seen here     ..................................................................................................................