Figure 5

Intra-species c e BLATs and composite- EvoPrints identify conserved sequences within the input reference DNA that have rearranged in the aligning regions of other genomes. A) Shown is a D. melanogaster (reference DNA) to D. virilis ceBLAT alignment that spans a 3,570 bp sequence located upstream of the fushi tarazu gene (-7184 to -3,434 bp from its transcription start). Black-colored uppercase nucleotides represent aligning bases found only in the highest scoring D. virilis eBLAT alignment, green-colored bases identify aligning bases that are unique to the second highest scoring alignment and blue-colored bases are aligning bases unique to the third highest score eBLAT alignment. B) Shown is an EvoPrint of the input D. melanogaster sequence shown in (A) that was generated with ceBLATs of the D. simulans, D. sechellia, D. yakuba, D. erecta, D. ananassae, D. pseudoobscura, D. persimilis, D. virilis, D. mojavensis, D. grimshawi and D. willistoni alignments. C) The accompanying EvoDifferences profile of the EvoPrint shown in (B). Black uppercase letters are aligning bases shared by all species examined. Colored uppercase letters, which denote individual species, represent sequences that were not aligned in the ceBLAT for just one of the genomes included in the analysis (D. simulans, teal; D. sechellia, dark-red; D. yakuba, brown; D. erecta, light-blue; D. ananassae, orange; D. pseudoobscura, pink; D. virilis, blue; D. mojavensis, green; or D. grimshawi, red).