Subclones: Transcript The clone libraries were prepared using bacterial artificial chromosomes, or BACs. Each BAC clone contained 100,000 to 200,000 bases of DNA sequence. The large BAC clones were used to establish the order of the DNA sequences. To sequence the DNA, smaller-sized clones were needed. Project scientists cut the large BAC clones into smaller fragments of about 2,000 bases. These smaller fragments were typically stored in viruses called phage that can infect E. coli cells.