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added sorting alignments documentation.
[jalview.git] / help / html / misc / geneticCode.html
diff --git a/help/html/misc/geneticCode.html b/help/html/misc/geneticCode.html
index 913de69..92c59d6 100755 (executable)
--- a/help/html/misc/geneticCode.html
+++ b/help/html/misc/geneticCode.html
@@ -1,8 +1,5 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
 <html>\r
-<head>\r
-<title>Untitled Document</title>\r
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">\r
+<head><title>Genetic Code</title>\r
 <style type="text/css">\r
 <!--\r
 td {\r
@@ -15,317 +12,58 @@ td {
 <body>\r
 \r
 \r
-<div align="center"> \r
+<div align="center">\r
   <h2>The Genetic Code </h2>\r
-  <table border="0">\r
-    <tr> \r
-      <td width="19%">&nbsp;</td>\r
-      <td width="60%">2nd Position</td>\r
-      <td width="21%">&nbsp;</td>\r
+  <table width="474" border="0">\r
+    <tr>\r
+      <td width="16%">&nbsp;</td>\r
+      <td width="70%">2nd Position</td>\r
+      <td width="14%">&nbsp;</td>\r
     </tr>\r
-    <tr> \r
+    <tr>\r
       <td><p>1st Position</p>\r
         <p>(5' end)</p></td>\r
       <td><table border=5 cellpadding=3>\r
-          <tr align=center bgcolor="#FFFFEE"> \r
-            <td></td>\r
-            <td><h2>U</h2></td>\r
-            <td><h2>C</h2></td>\r
-            <td><h2>A</h2></td>\r
-            <td><h2>G</h2></td>\r
-            <td></td>\r
+          <tr align=center bgcolor="#FFFFEE">\r
+            <td width="24"></td>\r
+            <td width="55"><h2>U</h2></td>\r
+            <td width="70"><h2>C</h2></td>\r
+            <td width="55"><h2>A</h2></td>\r
+            <td width="55"><h2>G</h2></td>\r
+            <td width="22"></td>\r
           </tr>\r
-          <tr align=center bgcolor="#FFFFEE"> \r
+          <tr align=center bgcolor="#FFFFEE">\r
             <td><h1>U</h1></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Phe</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Phe</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Leu</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Leu</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Ser</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ser</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ser</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ser</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Tyr</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Tyr</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>STOP</i></td>\r
-                </tr>\r
-                <tr> \r
-                  <td>STOP</i></td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Cys</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Cys</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>STOP</i></td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Trp</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>U</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>C</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>A</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>G</td>\r
-                </tr>\r
-              </table></td>\r
+            <td>Phe<br>Phe<br>Leu<br>Leu</td>\r
+                       <td>Ser<br>Ser<br>Ser<br>Ser</td>\r
+            <td>Tyr<br>Tyr<br>STOP</i><br>STOP</i></td>\r
+            <td>Cys<br>Cys<br>STOP</i><br>Trp</td>\r
+\r
+                        <td>U<br>C<br>A<br>G</td>\r
           </tr>\r
-          <tr bgcolor="#FFFFEE"> \r
+          <tr bgcolor="#FFFFEE">\r
             <td><h1>C</h1></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Leu</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Leu</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Leu</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Leu</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Pro</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Pro</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Pro</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Pro</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>His</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>His</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Gln</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Gln</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Arg</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Arg</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Arg</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Arg</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>U</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>C</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>A</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>G</td>\r
-                </tr>\r
-              </table></td>\r
+            <td>Leu<br>Leu<br>Leu<br>Leu</td>\r
+            <td>Pro<br>Pro<br>Pro<br>Pro</td>\r
+            <td>His<br>His<br>Gln<br>Gln</td>\r
+            <td>Arg<br>Arg<br>Arg<br>Arg</td>\r
+            <td>U<br>C<br>A<br>G</td>\r
           </tr>\r
-          <tr bgcolor="#FFFFEE"> \r
+          <tr bgcolor="#FFFFEE">\r
             <td><h1>A</h1></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Ile</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ile</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ile</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Met</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Thr</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Thr</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Thr</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Thr</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Asn</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Asn</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Lys</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Lys</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Ser</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ser</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Arg</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Arg</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>U</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>C</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>A</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>G</td>\r
-                </tr>\r
-              </table></td>\r
+            <td>Ile<br>Ile<br>Ile<br>Met</td>\r
+            <td>Thr<br>Thr<br>Thr<br>Thr</td>\r
+            <td>Asn<br>Asn<br>Lys<br>Lys</td>\r
+            <td>Ser<br>Ser<br>Arg<br>Arg</td>\r
+            <td>U<br>C<br>A<br>G</td>\r
           </tr>\r
-          <tr bgcolor="#FFFFEE"> \r
+          <tr bgcolor="#FFFFEE">\r
             <td><h1>G</h1></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Val</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Val</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Val</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Val</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Ala</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ala</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ala</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Ala</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Asp</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Asp</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Glu</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Glu</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>Gly</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Gly</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Gly</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>Gly</td>\r
-                </tr>\r
-              </table></td>\r
-            <td> <table border=0>\r
-                <tr> \r
-                  <td>U</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>C</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>A</td>\r
-                </tr>\r
-                <tr> \r
-                  <td>G</td>\r
-                </tr>\r
-              </table></td>\r
+            <td>Val<br>Val<br>Val<br>Val</td>\r
+            <td>Ala<br>Ala<br>Ala<br>Ala</td>\r
+            <td>Asp<br>Asp<br>Glu<br>Glu</td>\r
+            <td>Gly<br>Gly<br>Gly<br>Gly</td>\r
+            <td>U<br>C<br>A<br>G</td>\r
           </tr>\r
         </table></td>\r
       <td><p>3rd Position</p>\r