diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
index edba157916..f00ce2101f 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java
@@ -581,7 +581,7 @@ public static Last[][] setScoreVector(int x, int xb, int yb, int ye, int gep, in
 		if (x == xb) {
 			pointers = new Last[ye + 1][1];
 		} else {
-			pointers = new Last[ye + 1][];
+			pointers = new Last[ye + 1][1];
 			pointers[0] = new Last[1];
 			for (int y = 1; y < scores[x].length; y++) {
 				pointers[y][0] = setScorePoint(x, y, gep, subs[y], scores);
diff --git a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
index a50d8c4cde..169babaf04 100644
--- a/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
+++ b/biojava-alignment/src/test/java/org/biojava/nbio/alignment/TestDNAAlignment.java
@@ -165,4 +165,16 @@ public void testLinearAlignment() throws CompoundNotFoundException {
 		PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapP, matrix);
 		Assert.assertEquals(String.format("GTAAAA-G----------%nG-AAAACGTTTTTTTTTT%n"), aligner.getPair().toString());;
 	}
+	/**
+	* @author aegugup
+	*/
+	@Test
+	public void testLinearAlignmentLocal() throws CompoundNotFoundException {
+		DNASequence query = new DNASequence("TGTTACGG", DNACompoundSet.getDNACompoundSet());
+		DNASequence target = new DNASequence("GGTTGACTA", DNACompoundSet.getDNACompoundSet());
+		SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();
+		SimpleGapPenalty gapP = new SimpleGapPenalty((short)0, (short)8);
+		PairwiseSequenceAligner<DNASequence, NucleotideCompound> aligner = Alignments.getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapP, matrix);
+		Assert.assertEquals(String.format("GTT-AC%nGTTGAC%n"), aligner.getPair().toString());;
+	}
 }