                                                                        Gene putatively regulated by attenuation in S_flexneri_2a

                                                                        Characteristics of the secondary structures
Terminator:    Distance from promoter:119 nt.    Distance to gene:22 nt.     Distance to run of Ts=0 nt.   Size=25 nt.     Delta G=-18.60 kcal/mol
Antiterminator:    Distance from promoter:74 nt. Size=56 nt.     Delta G=-21.90 kcal/mol
Anti-antiterminator:    Distance from promoter:46 nt.    Size=51 nt.     Delta G=-14.44 kcal/mol

                                                                        Nomenclature/Definitions
The most likely promoter is: ttgaca-tactgt. It has a score value of 64.93 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

ttgacagcgtgaaaacagtacgggtactgtactaaagtcacttaaggaaacaaacATGAAACACATACCGTTTTTCTTCGC
ATTCTTTTTTACCTTCCCCTGAatgggaggcgtttcgtcgtgtgaaacagaatgcgaagacgaacaataaggcctcccaaatcg
gggggccttttttattgataacaaaaaggcaacactATG

    pheA Gene: pheA     GI: 24113938     BI number: SF2659     GOG: COG0077,COG1605     Description: chorismate mutase-P - prephenate dehydratas            ac           a  a           a  g           g  a            ta GA        gt T  a       tg C  t       gc Cg       |  g Cg       |  a Cg       |  a Ta        cg Tg        ta Cg        gc |  c       cg Cg        ta At       |  a T  t      |  c T  t      |  a T  c      |  a        a T  g      |  t      a  t T  t       ta       a  c T  c       ta        cg C  |      g  g       cg T  |       cg        cg Tg        gc        tg At        gc        cg Cg        at        cg Gt        gc        gc Cg        gc        gc Ta        gc        at Ta        ta        at                         ttttattgataacaaaaaggcaacactATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [E] COG0077 Prephenate dehydratase ... can be seen here [E] COG1605 Chorismate mutase ... can be seen here     ..................................................................................................................                                                                         Gene putatively regulated by attenuation in S_flexneri_2a                                                                         Characteristics of the secondary structures Terminator:    Distance to gene:201 nt.     Distance to run of Ts=0 nt.   Size=20 nt.     Delta G=-16.70 kcal/mol                                                                         Nomenclature/Definitions GCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAGtcctttatatt gagtgtatcgccaacgcgccttcgggcgcgttttttgttgacagcgtgaaaacagtacgggtactgtactaaagtcacttaaggaaacaaacATGAA ACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAatgggaggcgtttcgtcgtgtgaaa cagaatgcgaagacgaacaataaggcctcccaaatcggggggccttttttattgataacaaaaaggcaacactATG     pheA Gene: pheA     GI: 24113938     BI number: SF2659     GOG: COG0077,COG1605     Description: chorismate mutase-P - prephenate dehydratas           tc          t  g           cg           cg           gc           cg           gc           cg           at           at             ttttgttgacagcgtgaaaacagtacgggtactgtactaaagtcacttaaggaaacaaacATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAatgggaggcgtttcgtcgtgtgaaacagaatgcgaagacgaacaataaggcctcccaaatcggggggccttttttattgataacaaaaaggcaacactATG                                                                         Orthologous genes that have a predicted attenuator, grouped in COG families [E] COG0077 Prephenate dehydratase ... can be seen here [E] COG1605 Chorismate mutase ... can be seen here     ..................................................................................................................