diff --git a/src/JBrowse/View/Track/Alignments.js b/src/JBrowse/View/Track/Alignments.js
index 5a560c7827..d9c1573f2a 100644
--- a/src/JBrowse/View/Track/Alignments.js
+++ b/src/JBrowse/View/Track/Alignments.js
@@ -11,16 +11,17 @@ return declare( HTMLFeatures,
  */
 {
 
-    constructor: function() {
-    },
-
     _defaultConfig: function() {
         return Util.deepUpdate(
             dojo.clone( this.inherited(arguments) ),
-            { style: {
-                  className: 'alignment',
-                  arrowheadClass: 'arrowhead'
-              }
+            {
+                maxFeatureScreenDensity: 1.2,
+                layoutPitchY: 4,
+                style: {
+                    histScale: 1,
+                    className: 'alignment',
+                    arrowheadClass: 'arrowhead'
+                }
             }
         );
     },
diff --git a/src/JBrowse/View/Track/HTMLFeatures.js b/src/JBrowse/View/Track/HTMLFeatures.js
index 286c114095..f7fcb9d0ce 100644
--- a/src/JBrowse/View/Track/HTMLFeatures.js
+++ b/src/JBrowse/View/Track/HTMLFeatures.js
@@ -109,6 +109,10 @@ HTMLFeatures = declare( HTMLFeatures,
     _defaultConfig: function() {
         return {
             description: true,
+
+            maxFeatureScreenDensity: 0.5,
+            layoutPitchY: 6,
+
             style: {
                 className: "feature2",
                 histScale: 4,
@@ -412,18 +416,26 @@ HTMLFeatures = declare( HTMLFeatures,
             this._updatedLabelForBlockSize = blockBases;
         }
 
-        //console.log("scale: %d, histScale: %d", scale, this.histScale);
-        if( scale < stats.featureDensity * this.config.style.histScale ) {
-            // if our store offers density histograms, draw them
-            if( this.store.histograms ) {
+        // console.log(this.name+" scale: %d, density: %d, histScale: %d, screenDensity: %d", scale, stats.featureDensity, this.config.style.histScale, stats.featureDensity / scale );
+
+        // if we our store offers density histograms, and we are zoomed out far enough, draw them
+        if( this.store.histograms && scale < stats.featureDensity * this.config.style.histScale ) {
                 this.fillHist(blockIndex, block, leftBase, rightBase, stripeWidth,
                               containerStart, containerEnd);
-            }
-            // otherwise, display a zoomed-out-too-far message
-            else {
-                this.fillMessage( blockIndex, block, 'Too many features to show'+(scale >= this.browser.view.maxPxPerBp ? '': '; zoom in to see detail')+'.' );
-            }
-        } else {
+        }
+        // if we have no histograms, check the predicted density of
+        // features on the screen, and display a message if it's
+        // bigger than maxFeatureScreenDensity
+        else if( stats.featureDensity / scale > this.config.maxFeatureScreenDensity ) {
+            this.fillMessage(
+                blockIndex,
+                block,
+                'Too many features to show'
+                    + (scale >= this.browser.view.maxPxPerBp ? '': '; zoom in to see detail')
+                    + '.'
+            );
+        }
+        else {
 
             // if we have transitioned to viewing features, delete the
             // y-scale used for the histograms
@@ -650,7 +662,7 @@ HTMLFeatures = declare( HTMLFeatures,
             featureStart = parseInt(featureStart);
 
 
-        var levelHeight = this.glyphHeight + 2;
+        var levelHeight = this.glyphHeight;
 
         // if the label extends beyond the feature, use the
         // label end position as the end position for layout
@@ -664,11 +676,11 @@ HTMLFeatures = declare( HTMLFeatures,
         if( this.showLabels && scale >= this.labelScale ) {
             if (name) {
 	        featureEnd = Math.max(featureEnd, featureStart + (''+name).length * this.labelWidth / scale );
-                levelHeight += this.labelHeight;
+                levelHeight += this.labelHeight + 1;
             }
             if( description ) {
                 featureEnd = Math.max( featureEnd, featureStart + (''+description).length * this.labelWidth / scale );
-                levelHeight += this.labelHeight;
+                levelHeight += this.labelHeight + 1;
             }
         }
         featureEnd += Math.max(1, this.padding / scale);
@@ -956,7 +968,7 @@ HTMLFeatures = declare( HTMLFeatures,
     _getLayout: function( scale ) {
         // create the layout if we need to, and we can
         if( ( ! this.layout || this.layout.pitchX != 4/scale ) && scale )
-            this.layout = new Layout({pitchX: 4/scale, pitchY: 4});
+            this.layout = new Layout({pitchX: 4/scale, pitchY: this.layoutPitchY || this.config.layoutPitchY });
 
         return this.layout;
     },
@@ -964,7 +976,8 @@ HTMLFeatures = declare( HTMLFeatures,
         delete this.layout;
     },
 
-    // when all the blocks are hidden, we also should recalculate our layout 
+    // when all the blocks are hidden, we also should recalculate our
+    // layout
     changed: function() {
         this.inherited(arguments);
         this._clearLayout();