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<p>Abstract</p> <p>Background</p> <p>Reference genome sequences within the major taxa can be used to assist the development of genomic tools for related organisms. A major constraint in the use of these sequenced and annotated genomes is divergent evolution. Divergence of organisms from a common ancestor may have occurred millions of years ago, leading to apparently un-related and un-syntenic genomes when sequence alignment is attempted.</p> <p>Results</p> <p>A series of programs were written to prepare 36 Mbp of <it>Fusarium graminearum </it>sequence in 19 scaffolds as a reference genome. Exactly 4,152 Bacterial artificial chromosome (BAC) end sequences from 2,178 large-insert <it>Fusarium virguliforme </it>clones were tested against this sequence. A total of 94 maps of <it>F. graminearum </it>sequence scaffolds, annotated exonic fragments and associated <it>F. virguliforme </it>sequences resulted.</p> <p>Conclusion</p> <p>Developed here was a technique that allowed the comparison of genomes based on small, 15 bp regions of shared identity. The main power of this method lay in its ability to align <it>diverged </it>sequences. This work is unique in that discontinuous sequences were used for the analysis and information not readily apparent, such as match direction, are presented. The 94 maps and JAVA programs are freely available on the Web and by request.</p>