n BaraBLC1, the pHD-DsRed vector inserted 205bp upstream of the transcription start site without excising the BaraB gene itself. This results in a minor loss of expression. The attached alignment shows two separate Sanger sequencing reads aligned to the BaraB region. In one case, the alignment is a perfect match up until the promoter 206bp from the transcription start site, at which point it becomes vector sequence. In the other Sanger read, the alignment matches the BaraB promoter 205bp and closer, as well as the gene region, with some SNPs as noted.
In BaraBLC4, the pHD-DsRed vector inserted as intended given homology arms, replacing the BaraB coding sequence with the vector sequence, resulting in a BaraB null mutation.