Additional File 1.
The alignment between the DNA sequence of the D. melanogaster swi gene and the sequence of D. pseudoobscura contigs 2140 and 2139. For Drosophila melanogaster DNA sequence the coordinates of the FlyBase genome annotation (Release 3.1) were used. Identical nucleotides are marked with asterisks. The putative TATA box and characteristic CA and T nucleotides at the 5' region of swi are shown in red font. The 5' and 3' UTRs are marked in green, the coding part of the swi DNA sequence is marked in red. Note that the region of the first intron contains the number of small well conserved motifs. Those containing the NNATTA sequence, characteristic of homeobox protein binding sites, are marked in blue the others are marked in black. The very 3' part of the locus could be aligned with the complementary sequence of the 2139 contig due to the two stretches of extremely conserved DNA.
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Schwartz et al. BMC Genetics 2004 5:15 doi:10.1186/1471-2156-5-15