Allocated to a separate alignment block. Replaced the attribute of the second axis by the attribute of the axes.

public/app/plugins/panel/graph/axes_editor.html

@@ -31,16 +31,6 @@
 				</div>
 			</div>
 
-			<div class="gf-form-inline" ng-show="$index === 1">
-				<div class="gf-form">
-					<gf-form-switch class="gf-form" label="Align" tooltip="Align two Y-axes by {{yaxis.alignment ? yaxis.align || 0 : 'value'}}" label-class="width-6" switch-class="width-5" checked="yaxis.alignment" on-change="ctrl.render()"></gf-form-switch>
-				</div>
-				<div class="gf-form" ng-show="yaxis.alignment">
-					<label class="gf-form-label width-6">Value</label>
-					<input type="number" class="gf-form-input width-5" placeholder="0" ng-model="yaxis.align" ng-change="ctrl.render()" ng-model-onblur ng-init="yaxis.align = yaxis.align || 0">
-				</div>
-			</div>
-
 		<div ng-if="yaxis.show">
 			<div class="gf-form">
 				<label class="gf-form-label width-6">Decimals</label>
@@ -77,6 +67,16 @@
 			<input type="number" class="gf-form-input max-width-8" ng-model="ctrl.panel.xaxis.buckets" placeholder="auto" ng-change="ctrl.render()" ng-model-onblur bs-tooltip="'Number of buckets'" data-placement="right">
 		</div>
 
+		<div>
+			<br/>
+			<h5 class="section-heading">Y-Axes</h5>
+			<gf-form-switch class="gf-form" label="Align" tooltip="Align two Y-axes by {{ctrl.panel.yaxis.alignment ? ctrl.panel.yaxis.align || 0 : 'value'}}" label-class="width-6" switch-class="width-5" checked="ctrl.panel.yaxis.alignment" on-change="ctrl.render()"></gf-form-switch>
+			<div class="gf-form" ng-show="ctrl.panel.yaxis.alignment">
+				<label class="gf-form-label width-6">Value</label>
+				<input type="number" class="gf-form-input width-5" placeholder="0" ng-model="ctrl.panel.yaxis.align" ng-change="ctrl.render()" ng-model-onblur ng-init="ctrl.panel.yaxis.align = ctrl.panel.yaxis.align || 0">
+			</div>
+		</div>
+
 	</div>
 
 </div>

public/app/plugins/panel/graph/graph.ts

@@ -158,8 +158,8 @@ function graphDirective(timeSrv, popoverSrv, contextSrv) {
 
       function processRangeHook(plot) {
         var yaxis = plot.getYAxes();
-        if (yaxis.length > 1 && panel.yaxes[1].alignment) {
-          var align = panel.yaxes[1].align || 0;
+        if (yaxis.length > 1 && panel.yaxis.alignment) {
+          var align = panel.yaxis.align || 0;
           alignYLevel(yaxis, parseFloat(align));
         }
       }

public/app/plugins/panel/graph/module.ts

@@ -46,8 +46,6 @@ class GraphCtrl extends MetricsPanelCtrl {
         min: null,
         max: null,
         format: 'short',
-        alignment: false,
-        align: 0,
       },
     ],
     xaxis: {
@@ -57,6 +55,10 @@ class GraphCtrl extends MetricsPanelCtrl {
       values: [],
       buckets: null,
     },
+    yaxis: {
+      alignment: false,
+      align: 0,
+    },
     // show/hide lines
     lines: true,
     // fill factor