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\bibdata{all}
\bibcite{Abeles1986}{Abeles, 1986}
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\bibcite{Barrett.Sober1993}{Barrett {\em  et\nobreakspace  {}al.}, 1993}
\bibcite{Basharin1959}{Basharin, 1959}
\bibcite{Box1979}{Box, 1979}
\bibcite{Cheng.Kumar1993}{Cheng {\em  et\nobreakspace  {}al.}, 1993}
\bibcite{Day.McMorris1992}{Day \& McMorris, 1992}
\bibcite{deQueiroz1993}{de\nobreakspace  {}Queiroz, 1993}
\bibcite{Eagleman.Sejnowski2000}{Eagleman \& Sejnowski, 2000}
\bibcite{Fishel1993}{Fishel {\em  et\nobreakspace  {}al.}, 1993}
\bibcite{Gueron.Leroy1987}{Gu\'{e}ron {\em  et\nobreakspace  {}al.}, 1987}
\bibcite{Hengen.fisinfo}{Hengen {\em  et\nobreakspace  {}al.}, 1997}
\bibcite{Hubner1989b}{{H\"{u}bner} \& Arber, 1989}
\bibcite{Kendrick.Baldwin1987}{Kendrick \& Baldwin, 1987}
\bibcite{Klimasauskas1994}{Klima\v {s}auskas {\em  et\nobreakspace  {}al.}, 1994}
\bibcite{Kuhn1970}{Kuhn, 1970}
\bibcite{Leach1993}{Leach {\em  et\nobreakspace  {}al.}, 1993}
\bibcite{Leroy.Gueron1988}{Leroy {\em  et\nobreakspace  {}al.}, 1988}
\bibcite{Lewin1997}{Lewin, 1997}
\bibcite{Lisser1993}{Lisser \& Margalit, 1993}
\bibcite{Lyakhov.Schneider2001}{Lyakhov {\em  et\nobreakspace  {}al.}, 2001}
\bibcite{Miller1955}{Miller, 1955}
\bibcite{Nelson1993}{Nelson, 1993}
\bibcite{PappChattoraj1994}{Papp \& Chattoraj, 1994}
\bibcite{Papp.helixrepa}{Papp {\em  et\nobreakspace  {}al.}, 1993}
\bibcite{Pribnow1975}{Pribnow, 1975}
\bibcite{Purves.Nundy2002}{Purves {\em  et\nobreakspace  {}al.}, 2002}
\bibcite{Rager.Singer1998}{Rager \& Singer, 1998}
\bibcite{Reinisch1995}{Reinisch {\em  et\nobreakspace  {}al.}, 1995}
\bibcite{Robberson1990}{Robberson {\em  et\nobreakspace  {}al.}, 1990}
\bibcite{Roberts1995}{Roberts, 1995}
\bibcite{Roberts.Cheng1998}{Roberts \& Cheng, 1998}
\bibcite{Rogan.Faux.Schneider1998}{Rogan {\em  et\nobreakspace  {}al.}, 1998}
\bibcite{Rogan.Schneider.hmsh2.1995}{Rogan \& Schneider, 1995}
\bibcite{SchneiderPrimer}{Schneider, 1995}
\bibcite{Schneider.oxyr}{Schneider, 1996}
\bibcite{Schneider.ri}{Schneider, 1997{\em  {a}}}
\bibcite{Schneider.walker}{Schneider, 1997{\em  {b}}}
\bibcite{Schneider.ev2000}{Schneider, 2000}
\bibcite{Schneider.baseflip.2001}{Schneider, 2001}
\bibcite{Schneider.Zen2002}{Schneider, 2002}
\bibcite{Schneider.Mastronarde.malign}{Schneider \& Mastronarde, 1996}
\bibcite{Schneider.Stephens1990}{Schneider \& Stephens, 1990}
\bibcite{Schneider1986}{Schneider {\em  et\nobreakspace  {}al.}, 1986}
\bibcite{Seeman1976}{Seeman {\em  et\nobreakspace  {}al.}, 1976}
\bibcite{Shannon1948}{Shannon, 1948}
\bibcite{Slany.Kersten1992}{Slany \& Kersten, 1992}
\bibcite{Stephens.Schneider.Splice}{Stephens \& Schneider, 1992}
\bibcite{Verdine1994}{Verdine, 1994}
\bibcite{Zheng.Storz.oxyrfur1999}{Zheng {\em  et\nobreakspace  {}al.}, 1999}
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\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Sequence logos \cite  {Schneider.Stephens1990} for human donor and acceptor splice junctions \cite  {Stephens.Schneider.Splice} compared to the consensus sequence for both sites. Source: Adapted from \cite  {Stephens.Schneider.Splice}. }}{21}}
\newlabel{fig.splicelogo}{{1}{21}}
\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Sequence walkers \cite  {Schneider.walker} for a human acceptor site in the iduronidase synthetase gene and a mutation (indicated by an arrow). On the top sequence, the normal end of exon 4 is shown by a bracket and dashed line. The vertical rectangle on a sequence walker is the `zero base' used to identify the location of the walker. The vertical rectangles also indicate a scale from $-3$ to $+2$ bits. A 12.7 bit acceptor at 5154 directs splicing to the correct location. Source: Adapted from \cite  {Rogan.Faux.Schneider1998}.}}{22}}
\newlabel{fig.walker}{{2}{22}}
\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Sequence logo for random sequences.}}{23}}
\newlabel{fig.random}{{3}{23}}
\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Region upstream of the \emph  {tgt/sec} promoter of \emph  {E. coli} analyzed by Fis sequence walkers. The information for each Fis site was computed from models that are 21 bases wide ($-10$ to $+10$) but only the range $-7$ to $+7$ is shown by walkers. The sine waves represent major (peaks) and minor (valley) grooves faced by the Fis protein. Source: Adapted from \cite  {Schneider.walker}. }}{24}}
\newlabel{fig.tgtsec}{{4}{24}}
\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces Sequence logo for RepA binding sites.}}{25}}
\newlabel{fig.repalogo}{{5}{25}}
\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Sequence logo for the $-10$ region of \emph  {E. coli} promoters.}}{26}}
\newlabel{fig.minusten}{{6}{26}}
\@writefile{lof}{\contentsline {figure}{\numberline {7}{\ignorespaces Consensus \emph  {versus} $R_{sequence}$.}}{27}}
\newlabel{fig.rsco}{{7}{27}}
\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces $R_{sequence}$ and consensus information for sequence logos.}}{28}}
\newlabel{table.rsco}{{1}{28}}
