texshade 1.21 (2mar10)

git-svn-id: svn://tug.org/texlive/trunk@17314 c570f23f-e606-0410-a88d-b1316a301751

2 files changed, 676 insertions, 117 deletions

diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def
index a69d64f5d23..0f1931a541e 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.def
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.def
@@ -62,7 +62,7 @@
 \medsepline                         %  Medium height if separation line is on
 \medblockskip                       %  Medium skip between sequence blocks
 \flexblockspace                     %  Use optimized space between blocks
-\featurerule{0.5ex}                 %  Set feature rule thickness to 1/5 ex
+\featurerule{0.5ex}                 %  Set feature rule thickness to 1/2 ex
 \bargraphstretch{1}                 %  Do not stretch bars in feature graphs
 \colorscalestretch{1}               %  Do not stretch color scales in features
 \backtranstext{horizontal}          %  Horizontal triplets in feature texts
@@ -91,6 +91,10 @@
 \setseries{features}{md}            %  Use normal series for feature texts
 \setshape {features}{it}            %  Use italics shape for feature texts
 \setsize  {features}{normalsize}    %  Use normal size for feature texts
+\setfamily{featurestyles}{tt}       %  Use typewriter family for feature styles
+\setseries{featurestyles}{md}       %  Use normal series for feature styles
+\setshape {featurestyles}{up}       %  Use upright shape for feature styles
+\setsize {featurestyles}{normalsize}%  Use normal size for feature styles
 \setfamily{legend}{tt}              %  Use typewriter family for legend texts
 \setseries{legend}{md}              %  Use normal series for legend texts
 \setshape {legend}{up}              %  Use upright shape for legend texts
@@ -113,10 +117,10 @@
 \appearance{PHDtopo}{TM}{top}       %   |
      {box[LightGray]:TM\numcount}{} %   |
 \appearance{HMMTOP}{internal}       %   |
-           {bottom}{---}            %   |
+           {bottom}{'-'}            %   |
            {int.\ \Alphacount}      %   |
 \appearance{HMMTOP}{external}       %   |
-           {top}{---}               %   |
+           {top}{,-,}               %   |
            {ext.\ \Alphacount}      %   |
 \appearance{HMMTOP}{TM}{top}        %   |
            {helix}{TM\numcount}     %   |
diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty
index 646ce2b077e..d8ab1cccdc6 100644
--- a/Master/texmf-dist/tex/latex/texshade/texshade.sty
+++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty
@@ -8,13 +8,13 @@
 %% 
 %% LaTeX package for typesetting nucleotide and peptide alignments
 %% 
-%% Copyright (C) 1999-2009 Eric Beitz
+%% Copyright (C) 1999-2010 Eric Beitz
 %% See the file texshade.txt
 %% 
 
 \NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{texshade}[2009/10/05 LaTeX TeXshade (v1.20)]
-\message{Package `texshade', Version 1.20 of 2009/10/05.}
+\ProvidesPackage{texshade}[2010/03/01 LaTeX TeXshade (v1.21)]
+\message{Package `texshade', Version 1.21 of 2010/03/01.}
 
 \PassOptionsToPackage{dvips}{color}
 \PassOptionsToPackage{dvips}{graphicx}
@@ -112,12 +112,14 @@
 \newif\iftttopfeature \newif\ifbbbottomfeature
 \newif\ifttttopfeature\newif\ifbbbbottomfeature
 \newif\ifall@fshade   \newif\ifregionalemph
+\newif\ifregionallower
 \newif\ifframe@       \newif\ifregionaltint
 \newif\ifshow@logo    \newif\ifshow@sublogo
 \newif\ifhidechar     \newif\ifsh@wg@ps
 \newif\ifsimmode
 \newif\ifregionaltintnow
 \newif\ifregionalemphnow
+\newif\ifregionallowernow
 \newif\ifregionalshadenow
 \newif\iftopfeaturenow
 \newif\ifttopfeaturenow
@@ -138,7 +140,8 @@
 \def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:}
 \def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H}
 \def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n}
-\def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*}
+\def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*} \def\semic@n{;}
+\def\br@cket{[}
 \def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane}
 \def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}}
 \def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick}
@@ -2288,10 +2291,10 @@
                     \csname stack@@reg#1\endcsname}
       \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
                     \csname stack@@tintreg#1\endcsname}
-      \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
-                    \csname stack@@hidereg#1\endcsname}
       \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
                     \csname stack@@emphreg#1\endcsname}
+      \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
+                    \csname stack@@lowerreg#1\endcsname}
       \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
                     \csname stack@@framereg#1\endcsname}
       \expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
@@ -2341,10 +2344,10 @@
             \csname stack@reg\the\loopcount\endcsname}
          \expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{%
             \csname stack@tintreg\the\loopcount\endcsname}
-         \expandafter\xdef\csname stack@@hidereg\the\loopcount\endcsname{%
-            \csname stack@hidereg\the\loopcount\endcsname}
          \expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{%
             \csname stack@emphreg\the\loopcount\endcsname}
+         \expandafter\xdef\csname stack@@lowerreg\the\loopcount\endcsname{%
+            \csname stack@lowerreg\the\loopcount\endcsname}
          \expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{%
             \csname stack@framereg\the\loopcount\endcsname}
          \expandafter\xdef\csname stack@@top\the\loopcount\endcsname{%
@@ -2630,10 +2633,10 @@
             \csname stack@reg\the\innerloopcount\endcsname}
       \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
             \csname stack@tintreg\the\innerloopcount\endcsname}
-      \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{%
-            \csname stack@hidereg\the\innerloopcount\endcsname}
       \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
             \csname stack@emphreg\the\innerloopcount\endcsname}
+      \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
+            \csname stack@lowerreg\the\innerloopcount\endcsname}
       \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
             \csname stack@framereg\the\innerloopcount\endcsname}
       \expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
@@ -2909,7 +2912,8 @@
       \xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;%
                      \first@;\second@;\third@;\fourth@;\last@}
    \else
-      \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@stack
+      \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;}
+      \sort@stack
    \fi\fi
 }
 \def\get@regions#1..#2,#3@{%
@@ -2919,28 +2923,6 @@
    \sort@stack
    \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
 }
-\def\getregion@fromhidestack#1{%
-   \xdef\temp@{#1}
-   \xdef\first@{\csname stack@hidereg\temp@\endcsname}
-   \expandafter\get@fromstack\first@
-   \expandafter\xdef\csname hidestart\temp@\endcsname{\first@}
-   \expandafter\xdef\csname hidestop\temp@\endcsname{\second@}
-   \expandafter\xdef\csname hidestyle\temp@\endcsname{\third@}
-   \expandafter\xdef\csname hidetext\temp@\endcsname{\fourth@}
-   \expandafter\xdef\csname stack@hidereg\temp@\endcsname{\last@}
-}
-\def\sort@hidestack{%
-   \expandafter\get@fromstack\last@
-   \ifx\first@\ampers@nd
-      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;&;&;&;&;&;@}
-   \else
-   \ifnum\st@rt<\second@
-      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;%
-                     \first@;\second@;\third@;\fourth@;\last@}
-   \else
-      \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack
-   \fi\fi
-}
 \def\get@fromemphstack#1;#2;#3;#4@{%
    \xdef\first@{#1} \xdef\second@{#2}
    \xdef\third@{#3} \xdef\last@{#4@}
@@ -2973,6 +2955,34 @@
    \sort@emphstack
    \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
 }
+\def\getregion@fromlowerstack#1{%
+   \xdef\temp@{#1}
+   \xdef\first@{\csname stack@lowerreg\temp@\endcsname}
+   \expandafter\get@fromemphstack\first@
+   \expandafter\xdef\csname lowerstart\temp@\endcsname{\first@}
+   \expandafter\xdef\csname lowerstop\temp@\endcsname{\second@}
+   \expandafter\xdef\csname lowerall\temp@\endcsname{\third@}
+   \expandafter\xdef\csname stack@lowerreg\temp@\endcsname{\last@}
+}
+\def\sort@lowerstack{%
+   \expandafter\get@fromemphstack\last@
+   \ifx\first@\ampers@nd
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
+   \else
+   \ifnum\st@rt<\second@
+      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
+   \else
+      \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@lowerstack
+   \fi\fi
+}
+\def\get@lowerregions#1..#2,#3@{%
+   \regionallowertrue
+   \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
+   \xdef\last@{\csname stack@lowerreg\seq@\endcsname}
+   \xdef\tmpstack{}
+   \sort@lowerstack
+   \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
+}
 \def\get@fromdomstack#1;#2;#3@{%
    \xdef\first@{#1} \xdef\second@{#2}
    \xdef\last@{#3@}
@@ -3016,23 +3026,12 @@
    \expandafter\xdef\csname tintall\temp@\endcsname{\third@}
    \expandafter\xdef\csname stack@tintreg\temp@\endcsname{\last@}
 }
-\def\sort@tintstack{%
-   \expandafter\get@fromemphstack\last@
-   \ifx\first@\ampers@nd
-      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
-   \else
-   \ifnum\st@rt<\second@
-      \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
-   \else
-      \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@tintstack
-   \fi\fi
-}
 \def\get@tintregions#1..#2,#3@{%
    \regionaltinttrue
    \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
    \xdef\last@{\csname stack@tintreg\seq@\endcsname}
    \xdef\tmpstack{}
-   \sort@tintstack
+   \sort@emphstack
    \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack}
 }
 \def\getregion@fromframestack#1{%
@@ -3178,23 +3177,312 @@
       \fi%
    \fi%
 }
+\def\test@get#1#2@{%
+   \xdef\temp@{#1} \xdef\third@@{#2@}
+   \ifx\temp@\ampers@nd
+   \else
+      \if \temp@ X
+         \xdef\temp@{\second@@}
+      \fi
+      \ifx\temp@\second@@
+         \xdef\third@@{\second@@}
+      \else
+         \expandafter\test@get\third@@
+      \fi
+   \fi
+}
+\def\get@@second@#1#2@{\xdef\second@@{#1}\xdef\first@@{#2@}}
+\def\get@@third@#1]#2@{\xdef\third@@{#1&@}\xdef\fifth@@{#2@}}
+\def\get@third@#1#2@{\xdef\third@@{#1}\xdef\fifth@@{#2@}}
+\def\find@motif{%
+   \expandafter\get@@second@\first@@
+   \ifx\second@@\ampers@nd
+   \else
+      \ifx\second@@\d@t
+      \else
+         \advance\temp@count by 1
+         \if \third@@ X
+            \xdef\third@@{\second@@}
+         \fi
+         \ifx\third@@\br@cket
+            \expandafter\get@@third@\fifth@@
+            \expandafter\test@get\third@@
+         \fi
+         \ifx\second@@\third@@
+            \ifx\nineth@@\n@
+               \xdef\st@rt{\the\temp@count}
+               \xdef\st@p{n}
+            \fi
+            \xdef\nineth@@{y}
+            \expandafter\get@third@\fifth@@
+            \ifx\third@@\ampers@nd
+               \xdef\st@p{\the\temp@count}
+               \xdef\list@{}
+               \xdef\tmpstack{}
+               \xdef\temp@{shade}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@reg\seq@\endcsname}
+                  \loopcount=\style@
+                  \sort@stack
+                  \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{emph}
+               \ifx\temp@\temp@@
+                  \regionalemphtrue
+                  \xdef\last@{\csname stack@emphreg\seq@\endcsname}
+                  \sort@emphstack
+                  \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{lower}
+               \ifx\temp@\temp@@
+                  \regionallowertrue
+                  \xdef\last@{\csname stack@lowerreg\seq@\endcsname}
+                  \sort@lowerstack
+                  \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{tint}
+               \ifx\temp@\temp@@
+                  \regionaltinttrue
+                  \xdef\last@{\csname stack@tintreg\seq@\endcsname}     \message{((last:\last@))}
+                  \sort@emphstack
+                  \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} \message{((tmp:\tmpstack))}
+               \else
+               \xdef\temp@{frame}
+               \ifx\temp@\temp@@
+                  \frame@true
+                  \xdef\last@{\csname stack@framereg\seq@\endcsname}
+                  \sort@emphstack
+                  \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{ttttop}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@ttttop\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@ttttop\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{tttop}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@tttop\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@tttop\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{ttop}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@ttop\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@ttop\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{top}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@top\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@top\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{bottom}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@bottom\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@bottom\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{bbottom}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@bbottom\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@bbottom\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{bbbottom}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@bbbottom\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@bbbottom\seq@\endcsname{\tmpstack}
+               \else
+               \xdef\temp@{bbbbottom}
+               \ifx\temp@\temp@@
+                  \xdef\last@{\csname stack@bbbbottom\seq@\endcsname}
+                  \sort@fstack
+                  \expandafter\xdef\csname stack@bbbbottom\seq@\endcsname{\tmpstack}
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \fi
+               \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
+               \xdef\nineth@@{n}
+            \fi
+         \else
+            \xdef\nineth@@{n} \xdef\st@p{n}
+            \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
+         \fi
+      \fi
+   \find@motif
+   \fi
+}
+\def\prep@motif{%
+
+   \def\get@motif@specs##1,##2,##3,##4,##5,&{%
+      \xdef\seq@{##1} \xdef\temp@@{##2} \xdef\@ll{##3} \def\fourth@@{##4} \xdef\fifth@@{##5&@}
+   }
+
+   \loopcount=0
+   \loop
+      \advance\loopcount by 1
+      \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{\csname style\the\loopcount\endcsname;%
+                                                                 \csname start\the\loopcount\endcsname;%
+                                                                 \csname stop\the\loopcount\endcsname;%
+                                                                 \csname all\the\loopcount\endcsname;%
+                                                                 \csname stack@reg\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{\csname emphstart\the\loopcount\endcsname;%
+                                                                 \csname emphstop\the\loopcount\endcsname;%
+                                                                 \csname emphall\the\loopcount\endcsname;%
+                                                                 \csname stack@emphreg\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{\csname lowerstart\the\loopcount\endcsname;%
+                                                                 \csname lowerstop\the\loopcount\endcsname;%
+                                                                 \csname lowerall\the\loopcount\endcsname;%
+                                                                 \csname stack@lowerreg\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{\csname tintstart\the\loopcount\endcsname;%
+                                                                 \csname tintstop\the\loopcount\endcsname;%
+                                                                 \csname tintall\the\loopcount\endcsname;%
+                                                                 \csname stack@tintreg\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{\csname framestart\the\loopcount\endcsname;%
+                                                                 \csname framestop\the\loopcount\endcsname;%
+                                                                 \csname framestyle\the\loopcount\endcsname;%
+                                                                 \csname stack@framereg\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{\csname textttttop\the\loopcount\endcsname;%
+                                                                 \csname startttttop\the\loopcount\endcsname;%
+                                                                 \csname stopttttop\the\loopcount\endcsname;%
+                                                                 \csname stylettttop\the\loopcount\endcsname;%
+                                                                 \csname stack@ttttop\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{\csname texttttop\the\loopcount\endcsname;%
+                                                                 \csname starttttop\the\loopcount\endcsname;%
+                                                                 \csname stoptttop\the\loopcount\endcsname;%
+                                                                 \csname styletttop\the\loopcount\endcsname;%
+                                                                 \csname stack@tttop\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{\csname textttop\the\loopcount\endcsname;%
+                                                                 \csname startttop\the\loopcount\endcsname;%
+                                                                 \csname stopttop\the\loopcount\endcsname;%
+                                                                 \csname stylettop\the\loopcount\endcsname;%
+                                                                 \csname stack@ttop\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@top\the\loopcount\endcsname{\csname texttop\the\loopcount\endcsname;%
+                                                                 \csname starttop\the\loopcount\endcsname;%
+                                                                 \csname stoptop\the\loopcount\endcsname;%
+                                                                 \csname styletop\the\loopcount\endcsname;%
+                                                                 \csname stack@top\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{\csname textbottom\the\loopcount\endcsname;%
+                                                                 \csname startbottom\the\loopcount\endcsname;%
+                                                                 \csname stopbottom\the\loopcount\endcsname;%
+                                                                 \csname stylebottom\the\loopcount\endcsname;%
+                                                                 \csname stack@bottom\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{\csname textbbottom\the\loopcount\endcsname;%
+                                                                 \csname startbbottom\the\loopcount\endcsname;%
+                                                                 \csname stopbbottom\the\loopcount\endcsname;%
+                                                                 \csname stylebbottom\the\loopcount\endcsname;%
+                                                                 \csname stack@bbottom\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{\csname textbbbottom\the\loopcount\endcsname;%
+                                                                 \csname startbbbottom\the\loopcount\endcsname;%
+                                                                 \csname stopbbbottom\the\loopcount\endcsname;%
+                                                                 \csname stylebbbottom\the\loopcount\endcsname;%
+                                                                 \csname stack@bbbottom\the\loopcount\endcsname}
+      \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{\csname textbbbbottom\the\loopcount\endcsname;%
+                                                                 \csname startbbbbottom\the\loopcount\endcsname;%
+                                                                 \csname stopbbbbottom\the\loopcount\endcsname;%
+                                                                 \csname stylebbbbottom\the\loopcount\endcsname;%
+                                                                 \csname stack@bbbbottom\the\loopcount\endcsname}
+   \ifnum\loopcount<\seq@num\repeat
+   \temp@@count=0
+   \loop
+      \advance\temp@@count by 1
+      \xdef\first@@{\csname motif\the\temp@@count\endcsname}
+      \expandafter\get@motif@specs\first@@
+      \xdef\first@@{\csname sequence\seq@\endcsname &@}
+      \temp@count=\csname res@count\seq@\endcsname
+      \xdef\f@text@{\@ll}
+      \xdef\style@{\fourth@@}
+      \xdef\m@tif{\fifth@@} \expandafter\get@third@\fifth@@
+      \xdef\nineth@@{n} \xdef\st@p{n}
+      \find@motif
+   \ifnum\temp@@count<\motif@num\repeat
+   \loopcount=0
+   \loop
+      \advance\loopcount by 1
+      \expandafter\getregion@fromstack{\the\loopcount}
+      \expandafter\getregion@fromtintstack{\the\loopcount}
+      \expandafter\getregion@fromemphstack{\the\loopcount}
+      \expandafter\getregion@fromlowerstack{\the\loopcount}
+      \expandafter\getregion@fromframestack{\the\loopcount}
+      \xdef\bottop@{top}       \expandafter\getregion@fromfstack{\the\loopcount}
+      \xdef\bottop@{ttop}      \expandafter\getregion@fromfstack{\the\loopcount}
+      \xdef\bottop@{tttop}     \expandafter\getregion@fromfstack{\the\loopcount}
+      \xdef\bottop@{ttttop}    \expandafter\getregion@fromfstack{\the\loopcount}
+      \xdef\bottop@{bottom}    \expandafter\getregion@fromfstack{\the\loopcount}
+      \xdef\bottop@{bbottom}   \expandafter\getregion@fromfstack{\the\loopcount}
+      \xdef\bottop@{bbbottom}  \expandafter\getregion@fromfstack{\the\loopcount}
+      \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
+   \ifnum\loopcount<\seq@num\repeat
+}
+
+\def\test@motif#1#2@{%
+   \xdef\temp@{shade}
+   \ifx\temp@\temp@@ \xdef\style@{\the\loopcount} \fi
+   \xdef\temp@{emph}
+   \ifx\temp@\temp@@ \xdef\style@{0} \fi
+   \xdef\temp@{lower}
+   \ifx\temp@\temp@@ \xdef\style@{0} \fi
+   \xdef\temp@{tint}
+   \ifx\temp@\temp@@ \xdef\style@{0} \fi
+   \xdef\temp@{frame}
+   \ifx\temp@\temp@@ \xdef\style@{0} \fi
+   \xdef\temp@{#1#2}
+   \xdef\first@{#1}
+   \ifx\first@\br@cket
+      \xdef\label@motif{y}
+      \temp@count=\motif@num
+      \advance\temp@count by 1
+      \xdef\motif@num{\the\temp@count}
+      \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
+      \xdef\list@{&}
+   \else
+      \expandafter\check@char\first@
+      \ifletter
+         \xdef\label@motif{y}
+         \temp@count=\motif@num
+         \advance\temp@count by 1
+         \xdef\motif@num{\the\temp@count}
+         \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
+         \xdef\list@{&}
+      \fi
+   \fi
+}
 
 \def\test@PDB#1:#2,#3,#4,#5,#6@{%
    \xdef\last@{#1[,]&}\expandafter\opt@color\last@
+   \xdef\PDB@distance{no}
    \ifx\f@color\comm@
-      \xdef\PDB@distance{no}
    \else
       \xdef\f@color{\f@color .&&@}
       \expandafter\coord@get\f@color
-      \temp@count=\c@@rd
-      \multiply\temp@count by \temp@count
-      \xdef\PDB@distance{\the\temp@count}
+      \xdef\temp@{\c@@rd @}
+      \expandafter\check@letter\temp@
+      \ifletter
+      \else
+         \temp@count=\c@@rd
+         \multiply\temp@count by \temp@count
+         \xdef\PDB@distance{\the\temp@count}
+      \fi
    \fi
    \xdef\PDB@hitpos{0}
    \xdef\PDB@stack{}
    \xdef\PDB@name{#2}
    \xdef\PDB@type{point}
    \ifx\fourth@\PDB@type
+      \xdef\PDB@{y}
       \xdef\last@{#3[,]&}\expandafter\opt@color\last@
       \xdef\PDB@refnum@a{\fourth@}
       \ifx\f@color\C@lpha
@@ -3210,6 +3498,7 @@
    \else
       \xdef\PDB@type{line}
       \ifx\fourth@\PDB@type
+         \xdef\PDB@{y}
          \xdef\last@{#3[,]&}\expandafter\opt@color\last@
          \xdef\PDB@refnum{\fourth@}
          \ifx\f@color\C@lpha
@@ -3244,6 +3533,7 @@
       \else
          \xdef\PDB@type{plane}
          \ifx\fourth@\PDB@type
+            \xdef\PDB@{y}
             \xdef\last@{#3[,]&}\expandafter\opt@color\last@
             \xdef\PDB@refnum{\fourth@}
             \ifx\f@color\C@lpha
@@ -3299,6 +3589,9 @@
             \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
             \load@PDB
             \expandafter\get@item\PDB@stack \xdef\list@{\first@@}
+         \else
+            \xdef\temp@{\list@ @}
+            \expandafter\test@motif\temp@
          \fi
       \fi
    \fi
@@ -4952,11 +5245,15 @@
      \expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
      \expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
      \xdef\list@{#2,&}
+     \xdef\temp@@{shade}
      \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
-     \loop
-        \xdef\list@{\list@ @}
-        \expandafter\get@regions\list@
-     \ifx\list@\ampers@nd\else\repeat
+     \ifx\list@\ampers@nd
+     \else
+        \loop
+           \xdef\list@{\list@ @}
+           \expandafter\get@regions\list@
+        \ifx\list@\ampers@nd\else\repeat
+     \fi
    \fi
 }
 \def\shadeblock#1#2#3#4{%
@@ -4976,11 +5273,15 @@
    \else
      \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
      \xdef\list@{#2,&}
+     \xdef\temp@@{tint} \loopcount=0
      \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
-     \loop
-        \xdef\list@{\list@ @}
-        \expandafter\get@tintregions\list@
-     \ifx\list@\ampers@nd\else\repeat
+     \ifx\list@\ampers@nd
+     \else
+        \loop
+           \xdef\list@{\list@ @}
+           \expandafter\get@tintregions\list@
+        \ifx\list@\ampers@nd\else\repeat
+     \fi
    \fi
 }
 \def\tintblock#1#2{%
@@ -5006,6 +5307,34 @@
       \xdef\light@{LightLight}
    \fi\fi\fi
 }
+\def\lowerregion#1#2{%
+   \xdef\seq@{#1}
+   \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
+   \xdef\first@{\seq@ @} \expandafter\check@letter\first@
+   \xdef\first@{\seq@}
+   \ifletter \get@name@number \xdef\seq@{\first@} \fi
+   \ifnum\seq@>\seq@count
+     \message{<Ignored seq `\seq@' in \noexpand\lowerregion or \noexpand\lowerblock>}
+   \else
+     \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
+     \xdef\list@{#2,&}
+     \xdef\temp@@{lower} \loopcount=0
+     \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
+     \ifx\list@\ampers@nd
+     \else
+        \loop
+           \xdef\list@{\list@ @}
+           \expandafter\get@lowerregions\list@
+        \ifx\list@\ampers@nd\else\repeat
+     \fi
+   \fi
+}
+\def\lowerblock#1#2{%
+   \xdef\seq@{#1}
+      \xdef\@ll{yes}
+      \lowerregion{#1}{#2}
+      \xdef\@ll{}
+}
 \def\emphregion#1#2{%
    \xdef\seq@{#1}
    \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
@@ -5017,11 +5346,15 @@
    \else
      \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
      \xdef\list@{#2,&}
+     \xdef\temp@@{emph} \loopcount=0
      \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
-     \loop
-        \xdef\list@{\list@ @}
-        \expandafter\get@emphregions\list@
-     \ifx\list@\ampers@nd\else\repeat
+     \ifx\list@\ampers@nd
+     \else
+        \loop
+           \xdef\list@{\list@ @}
+           \expandafter\get@emphregions\list@
+        \ifx\list@\ampers@nd\else\repeat
+     \fi
    \fi
 }
 \def\emphblock#1#2{%
@@ -5042,11 +5375,15 @@
    \else
      \xdef\@ll{#3}
      \xdef\list@{#2,&}
+     \xdef\temp@@{frame} \loopcount=0
      \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
-     \loop
-        \xdef\list@{\list@ @}
-        \expandafter\get@frameregions\list@
-     \ifx\list@\ampers@nd\else\repeat
+     \ifx\list@\ampers@nd
+     \else
+        \loop
+           \xdef\list@{\list@ @}
+           \expandafter\get@frameregions\list@
+        \ifx\list@\ampers@nd\else\repeat
+     \fi
    \fi
 }
 \def\bargraphstretch#1{\def\b@r@stretch{#1}}
@@ -5429,8 +5766,6 @@
       \do@colorgraph
    \else
    \xdef\f@@color{\f@color}
-   \xdef\list@{#3,&}
-   \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
    \def\f@text@{#5}
    \xdef\f@color{\f@@color}
    \xdef\temp@{#4&}
@@ -5509,13 +5844,20 @@
       \fi
       \fi
       \fi
+   \xdef\list@{#3,&}
+   \xdef\@ll{\f@text@}
+   \xdef\temp@@{\bottop@}
+   \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
    \fi
    \loopcount=0
-   \loop
-      \advance\loopcount by 1\relax
-      \xdef\list@{\list@ @}
-      \expandafter\get@fregions\list@
-   \ifx\list@\ampers@nd\else\repeat
+   \ifx\list@\ampers@nd
+   \else
+      \loop
+         \advance\loopcount by 1\relax
+         \xdef\list@{\list@ @}
+         \expandafter\get@fregions\list@
+      \ifx\list@\ampers@nd\else\repeat
+   \fi
    \fi\fi\fi
    \fi
 }
@@ -7470,6 +7812,9 @@
            \xdef\first@{\csname res\the\loopcount\endcsname}
            \ifx\first@\equ@l
              \def\first@{\dom@char} \def\third@{9}
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+             \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
              \xdef\first@{=\first@}\fi
@@ -7499,6 +7844,9 @@
                     \fi
                     \fi
                  \fi
+                \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
                 \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7520,6 +7868,9 @@
                        \def\first@{{}} \def\third@{8}
                     \fi
                  \fi
+                \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
                 \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7533,6 +7884,9 @@
                \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
                \xdef\low@up{upper} \ifx\resn@m@tch\low@up
                \else \xdef\first@{\resn@m@tch} \fi\fi\fi
+               \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                  \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                  \xdef\first@{;\first@}\fi
                \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                   \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                   \xdef\first@{=\first@}\fi
@@ -7549,6 +7903,9 @@
        \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
        \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }}
        \else \xdef\first@{\n@m@tch} \fi\fi
+       \expandafter\ifx\csname lower@seq0\endcsname\y@
+          \expandafter\xdef\csname lower@seq0\endcsname{n}
+          \xdef\first@{;\first@}\fi
        \expandafter\ifx\csname tint@seq0\endcsname\y@
           \expandafter\xdef\csname tint@seq0\endcsname{n}
           \xdef\first@{=\first@}\fi
@@ -7579,6 +7936,9 @@
              \ifx\first@\d@t\def\first@{\gap@char}\fi
              \ifx\first@\questi@n\def\first@{\st@p@char}\fi
              \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7643,6 +8003,9 @@
               \fi
             \fi
           \fi
+          \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7657,6 +8020,9 @@
      \xdef\low@up{lower} \ifx\m@tch\low@up \make@lower \else
      \xdef\low@up{upper} \ifx\m@tch\low@up
      \else \xdef\first@{\m@tch} \fi\fi
+     \expandafter\ifx\csname lower@seq0\endcsname\y@
+                \expandafter\xdef\csname lower@seq0\endcsname{n}
+                \xdef\first@{;\first@}\fi
      \expandafter\ifx\csname tint@seq0\endcsname\y@
                 \expandafter\xdef\csname tint@seq0\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7678,6 +8044,9 @@
        \xdef\first@{\csname res\the\loopcount\endcsname}
        \ifx\first@\equ@l
           \def\first@{\dom@char} \def\third@{!}  \xdef\g@p{y}
+          \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\first@}\fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -7707,6 +8076,9 @@
                     \fi
                \fi
              \fi
+          \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\first@}\fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -7728,6 +8100,9 @@
                   \def\first@{{}} \def\third@{/}
                \fi
              \fi
+          \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\st@p@char}\fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\st@p@char}\fi
@@ -7740,6 +8115,9 @@
           \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
           \xdef\low@up{upper} \ifx\resn@m@tch\low@up
           \else \xdef\first@{\resn@m@tch} \fi\fi
+          \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\first@}\fi
           \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -7762,6 +8140,9 @@
              \ifx\first@\d@t\def\first@{\gap@char}\fi
              \ifx\first@\questi@n\def\first@{\st@p@char}\fi
              \ifx\first@\equ@l\def\first@{\dom@char}  \xdef\g@p{y} \fi
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7775,6 +8156,9 @@
          \xdef\first@{\csname res\the\loopcount\endcsname}
          \ifx\first@\equ@l
             \def\first@{\dom@char} \def\third@{9}  \xdef\g@p{y}
+           \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\first@}\fi
            \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -7804,6 +8188,9 @@
                     \fi
                \fi
             \fi
+           \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\first@}\fi
            \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -7825,6 +8212,9 @@
                        \def\first@{{}} \def\third@{8}
                \fi
             \fi
+           \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\first@}\fi
            \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -7838,6 +8228,9 @@
            \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else
            \xdef\low@up{upper} \ifx\resn@m@tch\low@up
            \else \xdef\first@{\resn@m@tch} \fi\fi\fi
+           \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                   \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                   \xdef\first@{;\first@}\fi
            \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                    \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                    \xdef\first@{=\first@}\fi
@@ -7854,6 +8247,9 @@
     \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else
     \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }}
     \else \xdef\first@{\n@m@tch} \fi\fi
+    \expandafter\ifx\csname lower@seq0\endcsname\y@
+                \expandafter\xdef\csname lower@seq0\endcsname{n}
+                \xdef\first@{;\first@}\fi
     \expandafter\ifx\csname tint@seq0\endcsname\y@
                 \expandafter\xdef\csname tint@seq0\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7879,6 +8275,9 @@
              \ifx\first@\d@t\def\first@{\gap@char}\fi
              \ifx\first@\questi@n\def\first@{\st@p@char}\fi
              \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7952,6 +8351,9 @@
                \fi
             \fi
     \fi
+    \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
     \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7966,6 +8368,9 @@
  \xdef\second@{lower} \ifx\m@tch\second@ \make@lower \else
  \xdef\second@{upper} \ifx\m@tch\second@
  \else \xdef\first@{\m@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+                \expandafter\xdef\csname lower@seq0\endcsname{n}
+                \xdef\first@{;\first@}\fi
  \expandafter\ifx\csname tint@seq0\endcsname\y@
                 \expandafter\xdef\csname tint@seq0\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -7990,6 +8395,9 @@
              \ifx\first@\d@t\def\first@{\gap@char}\fi
              \ifx\first@\questi@n\def\first@{\st@p@char}\fi
              \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8068,6 +8476,9 @@
                \fi
             \fi
     \fi
+    \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
     \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8082,6 +8493,9 @@
  \xdef\second@{lower} \ifx\@llm@tch\second@ \make@lower \else
  \xdef\second@{upper} \ifx\@llm@tch\second@
  \else \xdef\first@{\@llm@tch} \fi\fi
+ \expandafter\ifx\csname lower@seq0\endcsname\y@
+                \expandafter\xdef\csname lower@seq0\endcsname{n}
+                \xdef\first@{;\first@}\fi
  \expandafter\ifx\csname tint@seq0\endcsname\y@
                 \expandafter\xdef\csname tint@seq0\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8108,6 +8522,9 @@
         \xdef\third@{noshade}
         \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
              \xdef\first@{\csname res\the\loopcount\endcsname}
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8169,6 +8586,9 @@
          \fi
          \fi
         \fi
+        \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
         \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8227,6 +8647,9 @@
                  \make@lower \fi
      \xdef\third@{noshade}
      \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8237,6 +8660,9 @@
                 \csname seq\the\loopcount\endcsname%
                 0\first@}
      \else
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8292,6 +8718,9 @@
      \fi
      \xdef\third@{noshade}
      \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8302,6 +8731,9 @@
                 \csname seq\the\loopcount\endcsname%
                 *\first@}
      \else
+             \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+                \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
+                \xdef\first@{;\first@}\fi
              \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@
                 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8314,6 +8746,9 @@
      \fi
    \ifnum\loopcount<\seq@count \repeat
    \xdef\first@{\csname res0\endcsname}
+   \expandafter\ifx\csname lower@seq0\endcsname\y@
+                \expandafter\xdef\csname lower@seq0\endcsname{n}
+                \xdef\first@{;\first@}\fi
    \expandafter\ifx\csname tint@seq0\endcsname\y@
                 \expandafter\xdef\csname tint@seq0\endcsname{n}
                 \xdef\first@{=\first@}\fi
@@ -8441,6 +8876,56 @@
       \fi
 }
 
+\def\getregion@fromlowerstack@first{%
+      \expandafter\getregion@fromlowerstack{\the\loopcount}
+      \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+      \else
+      \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@
+         \getregion@fromlowerstack@first
+      \else
+         \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@
+            \innerloopcount=1
+         \fi
+         \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+      \fi
+      \fi
+}
+
+\def\calc@reglower{%
+      \loopcount=-1 \innerloopcount=0
+      \loop
+         \advance\loopcount by 1
+         \ifnum\loopcount=0 \xdef\first@@{\the\cons@count}
+         \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi
+         \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+         \else
+         \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>\first@@
+         \else
+            \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@
+              \getregion@fromlowerstack@first
+            \else
+               \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@
+                  \innerloopcount=1
+               \fi
+               \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+               \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname=\first@@
+                  \expandafter\getregion@fromlowerstack{\the\loopcount}
+               \fi
+            \fi
+         \fi\fi
+      \ifnum\loopcount<\seq@count \repeat
+      \loopcount=0
+      \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@
+         \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+      \fi
+      \ifnum\innerloopcount>0
+         \loop
+            \advance\loopcount by 1
+            \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y}
+         \ifnum\loopcount<\seq@count \repeat
+      \fi
+}
+
 \def\getregion@fromtintstack@first{%
       \expandafter\getregion@fromtintstack{\the\loopcount}
       \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd
@@ -8728,6 +9213,59 @@
    \xdef\second@@@{\csname res\the\innerloopcount\endcsname}
    \xdef\third@@@{\csname cons\first@@@\second@@@\endcsname}
    \advance\temp@count by \third@@@
+   \ifnum\innerloopcount<\seq@count\sum@up\fi
+}
+
+\def\sum@up@cons{%
+   \innerloopcount=\outerloopcount
+   \xdef\first@@@{\csname res\the\outerloopcount\endcsname}
+   \sum@up
+   \advance\outerloopcount by 1\relax
+   \ifnum\outerloopcount<\seq@count
+      \sum@up@cons
+   \else
+      \innerloopcount=\seq@count
+      \advance\innerloopcount by -1
+      \multiply\innerloopcount by \seq@count
+      \multiply\temp@count by 2
+      \multiply\temp@count by \m@trixf@ctor
+      \divide\temp@count by \innerloopcount
+
+      \ifnum\temp@count>100 \temp@count=100 \fi
+      \ifnum\temp@count<0   \temp@count=0 \fi
+      \xdef\cons@val{\the\temp@count}
+      \ifx\first@\equ@l \xdef\cons@val{N} \fi
+
+      \ifx\T@coffee@bcons\y@
+         \xdef\cons@val{\csname TC@num0\endcsname}
+         \if\cons@val *
+            \xdef\cons@val{99}
+         \fi
+      \fi
+      \ifx\T@coffee@ccons\y@
+         \xdef\cons@val{\csname TC@num0\endcsname}
+         \if\cons@val *
+            \xdef\cons@val{99}
+         \fi
+      \fi
+   \fi
+}
+
+\def\collect@cons@res{%
+   \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname}
+   \advance\innerloopcount by 1
+   \ifnum\innerloopcount>\seq@count\relax
+      \outerloopcount=1\relax
+      \temp@count=0\relax
+      \sum@up@cons
+   \else
+      \collect@cons@res
+   \fi
+}
+
+\def\sum@@up{%
+   \advance\innerloopcount by 1
+   \xdef\second@@@{\csname res\the\innerloopcount\endcsname}
 
    \ifx\first@@@\d@t
    \else
@@ -8765,55 +9303,31 @@
     \fi
    \fi
 
-   \ifnum\innerloopcount<\seq@count\sum@up\fi
+   \ifnum\innerloopcount<\seq@count\sum@@up\fi
 }
 
-\def\sum@up@cons{%
+\def\sum@up@sim{%
    \innerloopcount=\outerloopcount
    \xdef\first@@@{\csname res\the\outerloopcount\endcsname}
-   \sum@up
+   \sum@@up
    \advance\outerloopcount by 1\relax
    \ifnum\outerloopcount<\seq@count
-      \sum@up@cons
-   \else
-      \innerloopcount=\seq@count
-      \advance\innerloopcount by -1
-      \multiply\innerloopcount by \seq@count
-      \multiply\temp@count by 2
-      \multiply\temp@count by \m@trixf@ctor
-      \divide\temp@count by \innerloopcount
-
-      \ifnum\temp@count>100 \temp@count=100 \fi
-      \ifnum\temp@count<0   \temp@count=0 \fi
-      \xdef\cons@val{\the\temp@count}
-      \ifx\first@\equ@l \xdef\cons@val{N} \fi
-
-      \ifx\T@coffee@bcons\y@
-         \xdef\cons@val{\csname TC@num0\endcsname}
-         \if\cons@val *
-            \xdef\cons@val{99}
-         \fi
-      \fi
-      \ifx\T@coffee@ccons\y@
-         \xdef\cons@val{\csname TC@num0\endcsname}
-         \if\cons@val *
-            \xdef\cons@val{99}
-         \fi
-      \fi
+      \sum@up@sim
    \fi
 }
 
-\def\collect@cons@res{%
+\def\collect@similarity{%
    \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname}
    \advance\innerloopcount by 1
    \ifnum\innerloopcount>\seq@count\relax
       \outerloopcount=1\relax
       \temp@count=0\relax
-      \sum@up@cons
+      \sum@up@sim
    \else
-      \collect@cons@res
+      \collect@similarity
    \fi
 }
+
 \def\sum@up@bits{%
    \ifx\first@@@\second@@@
       \ifx\first@@@\d@t
@@ -10035,6 +10549,7 @@
     \ifregionalshadenow \calc@regshade \fi
     \ifregionaltintnow  \calc@regtint  \fi
     \ifregionalemphnow  \calc@regemph  \fi
+    \ifregionallowernow \calc@reglower \fi
     \ifframenow         \calc@frame    \fi
     \iftopfeaturenow       \xdef\bottop@{top}       \calc@feature \fi
     \ifttopfeaturenow      \xdef\bottop@{ttop}      \calc@feature \fi
@@ -10044,6 +10559,7 @@
     \ifbbottomfeaturenow   \xdef\bottop@{bbottom}   \calc@feature \fi
     \ifbbbottomfeaturenow  \xdef\bottop@{bbbottom}  \calc@feature \fi
     \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi
+    \ifnum\seq@count>1 \innerloopcount=1 \collect@similarity \fi
     \advance\pos@count by 1
      \ifshow@logo         \calc@logo     \fi
      \ifall@fshade \all@funcshade
@@ -10193,11 +10709,20 @@
             \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>%
             \innerloopcount
             \else
-            \else
                   \regionalemphnowtrue
             \fi
          \fi
     \fi
+    \ifregionallower
+         \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+         \else
+            \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>%
+            \innerloopcount
+            \else
+                  \regionallowernowtrue
+            \fi
+         \fi
+    \fi
     \ifframe@
          \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd
          \else
@@ -10353,7 +10878,7 @@
     \else
          \innerloopcount=\csname res@count\the\loopcount\endcsname
          \advance\innerloopcount by \res@perline
-    \fi              %%%%%%%%%%%%%*****
+    \fi
     \advance\innerloopcount by 1
     \ifregionalshade
          \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd
@@ -10385,6 +10910,16 @@
             \fi
          \fi
     \fi
+    \ifregionallower
+         \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd
+         \else
+            \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>%
+            \innerloopcount
+            \else
+               \regionallowernowtrue
+            \fi
+         \fi
+    \fi
     \ifframe@
          \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd
          \else
@@ -10799,6 +11334,14 @@
          \xdef\temp@@{\light@}%
          \expandafter\get@second@\first@%
    \fi%
+   \ifx\second@\semic@n%
+         \expandafter\get@second@\first@%
+         \xdef\first@@{\first@}%
+         \xdef\first@{\second@}%
+         \make@lower%
+         \xdef\second@{\first@}%
+         \xdef\first@{\first@@}%
+   \fi%
    \textcolor{\temp@@\boxc@l@r}{\box@rule}%
    \ifhidechar%
       \ifx\second@\o@%
@@ -10903,6 +11446,14 @@
    \else%
          \def\temp@{\csname relax\endcsname}%
    \fi%
+   \ifx\second@\semic@n%
+         \expandafter\get@second@\first@%
+         \xdef\first@@{\first@}%
+         \xdef\first@{\second@}%
+         \make@lower%
+         \xdef\second@{\first@}%
+         \xdef\first@{\first@@}%
+   \fi%
    \textcolor{\boxc@l@r}{\box@rule}%
    \ifhidechar%
       \ifx\second@\o@%
@@ -12963,7 +13514,7 @@
           \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
           \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
           \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
-          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
        \ifnum\loopcount<\seq@count\repeat
        \xdef\domain@num@list{}
        \xdef\last@{\stack@dom}
@@ -13012,6 +13563,7 @@
      \fi
      \ifshow@sublogo \prep@sublogo \fi
      \ifshow@logo  \prep@logo  \fi
+     \ifx\label@motif\y@  \prep@motif \fi
      \ifnum\seq@pointer>\res@perline \block@output \fi
     \else \read@loop
     \fi}
@@ -13063,7 +13615,7 @@
           \expandafter\xdef\csname sequence\the\loopcount\endcsname{}
           \expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
           \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
-          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
+          \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
        \ifnum\loopcount<\seq@count\repeat
        \xdef\domain@num@list{}
        \xdef\last@{\stack@dom}
@@ -13112,6 +13664,7 @@
      \fi
      \ifshow@sublogo \prep@sublogo \fi
      \ifshow@logo  \prep@logo  \fi
+     \ifx\label@motif\y@  \prep@motif \fi
      \ifnum\seq@pointer>\res@perline \block@output \fi
     \else
        \read@fasta
@@ -13245,8 +13798,8 @@
     \expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
-    \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
+    \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
     \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
     \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
     \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -13266,6 +13819,7 @@
        \cleanup@name
        \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
        \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
+       \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
        \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false}
        \expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false}
        \expandafter\xdef\csname hide@name\the\loopcount\endcsname{no}
@@ -13274,8 +13828,8 @@
        \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes}
        \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
        \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
-       \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@}
        \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
+       \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
        \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
        \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
        \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
@@ -13322,9 +13876,9 @@
    \ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi
    \loopcount=0
    \expandafter\getregion@fromstack{\the\loopcount}
-   \expandafter\getregion@fromhidestack{\the\loopcount}
    \expandafter\getregion@fromtintstack{\the\loopcount}
    \expandafter\getregion@fromemphstack{\the\loopcount}
+   \expandafter\getregion@fromlowerstack{\the\loopcount}
    \expandafter\getregion@fromframestack{\the\loopcount}
    \xdef\bottop@{top}       \expandafter\getregion@fromfstack{\the\loopcount}
    \xdef\bottop@{ttop}      \expandafter\getregion@fromfstack{\the\loopcount}
@@ -13373,9 +13927,9 @@
           \baselineskip=\box@height \advance\baselineskip by \box@depth
        \fi
        \expandafter\getregion@fromstack{\the\loopcount}
-       \expandafter\getregion@fromhidestack{\the\loopcount}
        \expandafter\getregion@fromtintstack{\the\loopcount}
        \expandafter\getregion@fromemphstack{\the\loopcount}
+       \expandafter\getregion@fromlowerstack{\the\loopcount}
        \expandafter\getregion@fromframestack{\the\loopcount}
        \xdef\bottop@{top}       \expandafter\getregion@fromfstack{\the\loopcount}
        \xdef\bottop@{ttop}      \expandafter\getregion@fromfstack{\the\loopcount}
@@ -13607,7 +14161,7 @@
 \cons@count=0
 \expandafter\xdef\csname res@count0\endcsname{0}
 \xdef\allow@zero{n} \xdef\c@ns@shift{0}
-\regionalshadefalse\regionalemphfalse\regionaltintfalse
+\regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse
 \frame@false
 \xdef\ruler@rot{0}
 \topfeaturefalse    \bottomfeaturefalse
@@ -13716,7 +14270,8 @@
 \xdef\all@thresh@ld{100}  \all@shadefalse
 \hidefeaturenames         \hidefeaturestylenames
 \xdef\T@coffee@ccons{n}   \xdef\T@coffee@bcons{n}
-\xdef\dom@in{no}
+\xdef\dom@in{no}          \xdef\label@motif{no}
+\xdef\motif@num{0}
 \hfuzz9999pt
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%