Plot of transposase transcript RPKM values against previously determined transposase gene clusters. Scale on the bottom represents the genome coordinates in Mb. The red line indicates the density of transposase ORFs in a 250 kb moving window in the CcI3 genome. Blue bars indicate RPKM values of each transposase ORF in the indicated growth conditions. The dotted line indicates the median RPKM value for all ORFs within the sample. Grey boxes indicate previously determined active deletion windows . An IS66 transposase transcript having an RPKM value greater than 1600 in all three samples is indicated with a broken line.