In vivo DNA binding of 21 sequence-specific and 2 general transcription factors to the even skipped (eve) and snail (sna) loci. ChIP/chip scores are plotted for 675-bp windows associated with all oligonucleotides on the array in the portions of the genome shown. In those regions bound above the 1% FDR threshold, the plots are colored green (Early A-P factors), yellow (Pair rule A-P factors), blue (D-V factors) or red (General factors). The locations of major RNA transcripts are shown below (blue) for both DNA strands together with the locations of CRMs active in blastoderm embryos (green) and later stages of development (salmon). Nucleotide coordinates in the genome are given in base-pairs. At the bottom is show the mRNA expression patterns of eve and sna in mid-stage 5 blastoderm embryos from the BDTNP's VirtualEmbryo using PointCloudXplore [12, 69]. A more detailed plot comparing ChIP scores for both factor and negative control immunoprecipitations is shown in Additional data file 14, including data for all antibodies shown in Table 2.