                                                                        Gene putatively regulated by attenuation in Buchnera_sp

                                                                        Characteristics of the secondary structures
Terminator:    Distance to gene:142 nt.     Distance to run of Ts=0 nt.   Size=24 nt.     Delta G= -6.70 kcal/mol
Antiterminator: Size=73 nt.     Delta G= -5.50 kcal/mol
Anti-antiterminator:   Size=54 nt.     Delta G= -7.40 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

TTGATCTGCAATTTTATCTGGATGGCCTTCTGAAACTGATTCAGATGTAAAAAGATAC
TCGGTCATtttatatatttaccttattttaaaataattgtatctttatatttttaagaaacaaaaataaatgtagtatagattaagatctatat
tgtttttaatttacaaaaaagtcttactttattataatattttttatatataaaaaaattacaaatagatatttattattaatatataaaatataatata
ttttttaacataaaaaaacgatatgtttttattttttaataacaacatATT

    endA --- yggJ Gene: endA     GI: 15617011     BI number: BU409     GOG: COG2356     Description: endonuclease I Gene: yggJ     GI: 15617012     BI number: BU410     GOG: COG1385     Description: hypothetical protei             t           a  t           t  t           a  t           t  t            ta            ta            cg            ta           a  a            ta            gc            ta           t  |   a       a  | t  c      a  | t  c      t  | t  t      a  | at       a  | ta       a  | at       a  | |  t       ta t  t       ta at        ta ta        ta ta        at ta        ta Ta        ta At       |  a C  a      c  t Ta        cg Gt        at        aa G  t       ta       t  g C  |      t  |       ta T  |      t  |       at Cg       a  |       gc At        tg        at Ta        at        ta At        ta        at Gc        at        ta At        ta        gt At        tg        at At        ta        tg                         tttttaatttacaaaaaagtcttactttattataatattttttatatataaaaaaattacaaatagatatttattattaatatataaaatataatatattttttaacataaaaaaacgatatgtttttattttttaataacaacatATT                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [L] COG2356 Endonuclease I ... can be seen here [S] COG1385 Uncharacterized protein conserved in bacteria ... can be seen here     ..................................................................................................................