NGS has become a popular research field in biologists because it was able to produce inexpensive and accuracy short biology sequences very fast. NGS technique has been improved to produce long length sequences, more than 100bp, recently with the same quality, accuracy and speed. Thus, tools for short sequences may be not suitable for long length sequences. We propose a new tool called UNION for re-sequencing applications by mapping long length sequences to a reference genome. UNION uses the UniMarker with a non-overlapping interval indexing strategy and a tool, CORAL, to do sequence alignments. For the experiments we randomly cut ten thousands sequences with a length of 512bp from the genome of Trichomonas and also produce mutations/sequence errors for these sequences to simulate different similarities. UNION has been compared with GMAP in terms of speed and accuracy and achieves better performance than that of GMAP.