Index: etc/mast-to-html.xsl
===================================================================
--- etc/mast-to-html.xsl	(revision 4530)
+++ etc/mast-to-html.xsl	(working copy)
@@ -395,6 +395,12 @@
           seqDispSeq.style.height = "1.5em";
           return seqDispSeq; 
         }
+        function annobox_boundary() {
+          var seqDispSeq = document.createElement('div');
+          seqDispSeq.className = "sequence";
+          seqDispSeq.style.height = "1.5em";
+          return seqDispSeq; 
+        }
 
         function create_seq_handle(container, seqid, isleft, pos, max) {
           var vbar = document.createElement('div');
@@ -557,7 +563,7 @@
         function set_data(start, width, show_rc_only, data, annobox) {
           var child = annobox.firstChild;
           var line_width = Math.min(wrap, width);
-          var num_per_wrap = <xsl:choose><xsl:when test="/mast/model/translate_dna/@value = 'y'">5</xsl:when><xsl:otherwise>4</xsl:otherwise></xsl:choose>;
+          var num_per_wrap = <xsl:choose><xsl:when test="/mast/model/translate_dna/@value = 'y'">6</xsl:when><xsl:otherwise>5</xsl:otherwise></xsl:choose>;
           var end = start + width;
           for (var i = start; i &lt; end; i += line_width, line_width = Math.min(wrap, end - i)) {
             for (var j = 0; j &lt; num_per_wrap; ++j) {
@@ -575,13 +581,23 @@
                   child = annobox_matches();
                   break;
                 case 3:
-      <xsl:if test="/mast/model/translate_dna/@value = 'y'">
+      <xsl:choose>
+        <xsl:when test="/mast/model/translate_dna/@value = 'y'">
                   child = annobox_translations();
                   break;
                 case 4:
-      </xsl:if>
                   child = annobox_sequence();
                   break;
+                case 5:
+        </xsl:when>
+        <xsl:otherwise>
+                  child = annobox_sequence();
+                  break;
+                case 4:
+        </xsl:otherwise>
+      </xsl:choose>
+                  child = annobox_boundary();
+                  break;
                 }
                 annobox.appendChild(child);
               }
@@ -596,13 +612,23 @@
                 data.append_matches(child, i, line_width, show_rc_only);
                 break;
               case 3:
-      <xsl:if test="/mast/model/translate_dna/@value = 'y'">
+      <xsl:choose>
+        <xsl:when test="/mast/model/translate_dna/@value = 'y'">
                 data.append_translation(child, i, line_width, show_rc_only);
                 break;
               case 4:
-      </xsl:if>
                 data.append_seq(child, i, line_width, show_rc_only);
                 break;
+              case 5:
+        </xsl:when>
+        <xsl:otherwise>
+                data.append_seq(child, i, line_width, show_rc_only);
+                break;
+              case 4:
+        </xsl:otherwise>
+      </xsl:choose>
+                data.append_boundary(child, i, line_width, show_rc_only);
+                break;
               }
               child = child.nextSibling;
             }
@@ -870,6 +896,7 @@
           this.append_hits = Sequence_append_hits;
           this.append_matches = Sequence_append_matches;
           this.append_labels = Sequence_append_labels;
+          this.append_boundary = Sequence_append_boundary;
           //init
           var mysegs = document.getElementById(seqid + "_segs");
           var lines = mysegs.value.split(/\n/);
@@ -1176,6 +1203,47 @@
           container.appendChild(oTable);
 
         }
+
+        function Sequence_append_boundary(container, start, width, is_rc) {
+          if (start &gt; this.length) {
+            alert("start: " + start + " length: " + this.length);
+            throw "INDEX_OUT_OF_BOUNDS";
+          }
+          if ((start + width - 1) &gt; this.length) {
+            alert("start: " + start + " width: " + width + " length: " + this.length);
+            throw "RANGE_OUT_OF_BOUNDS";
+          }
+          //make a sub container to put the sequence in
+          var mycontainer = document.createElement('span');
+          var pos = start;
+          var text = "";
+          var iter = this.get_overlapping_hits(start, width, is_rc);
+          while (iter.has_next()) {
+            var o = iter.next();
+            var end;
+            while (o.start &gt; pos) {
+              text += "&nbsp;";
+              ++pos;
+            }
+            if (o.start == o.hit.pos) {
+              text += "\\";
+              ++pos;
+            }
+            end = o.start + o.length - 1;
+            while (end &gt; pos) {
+              text += "_";
+              ++pos;
+            }
+            if (end == (o.hit.pos + o.hit.width -1)) {
+              text += "/"
+            } else {
+              text += "_"
+            }
+            ++pos;
+          }
+          mycontainer.appendChild(document.createTextNode(text));
+          container.appendChild(mycontainer);
+        }
         //+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
         // End Sequence Object
         //+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@@ -1992,7 +2060,7 @@
             <xsl:value-of select="@pos" /><xsl:text>&tab;</xsl:text> 
             <xsl:value-of select="@motif" /><xsl:text>&tab;</xsl:text>
             <xsl:choose>
-              <xsl:when test="@strand = 'forward'">
+              <xsl:when test="not (@strand) or @strand = 'forward'">
                 <xsl:text>+</xsl:text>
               </xsl:when>
               <xsl:otherwise>