@Test
public void testMatchesNoMatches() throws Exception {

    GappedSequence mismatch = DNATools.createGappedDNASequence("gggggggggggggggggggg", "mismatch");
    AlignmentPair allMismatches = new AlignmentPair(mismatch, subject, substitutionMatrix);
    assertEquals(Collections.<Range<Long>>emptyList(), matches(allMismatches));
}