diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 8bf462b..1c62872 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -23,6 +23,7 @@ public class Simulator implements GraphModificationFunctions {
     private static final int cdr1AlphaIndex = 2;
     private static final int cdr1BetaIndex = 3;
 
+
     //Make the graph needed for matching CDR3s
     public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
         Instant start = Instant.now();
@@ -34,7 +35,7 @@ public class Simulator implements GraphModificationFunctions {
 
         if(verbose){System.out.println("Making cell maps");}
         //HashMap keyed to Alphas, values Betas
-        Map<Integer, Integer> distCellsMapAlphaKey = makeSequenceToSequenceMap(distinctCells, 0, 1);
+        Map<Integer, Integer> distCellsMapAlphaKey = makeSequenceToSequenceMap(distinctCells, cdr3AlphaIndex, cdr3BetaIndex);
         if(verbose){System.out.println("Cell maps made");}
 
         if(verbose){System.out.println("Making well maps");}