Characterization of CR1 repeats. (A) Phylogenetic analysis of 332 CR1 sequences. The sequences used cover ∼450 bp of the 3′ terminus of the element. Bootstrap values for the major branches are indicated. (B) Size distribution of 96,230 CR1 elements found in the chicken genome. The vast majority of the copies are fragments shorter than 1000 bp. (C) Sequence organization of a putative intact CR1-F mother element. The element consists of two closely spaced ORFs (ORF-1 and ORF-2), 4 bp of 5′ UTR, and 103 bp of 3′ UTR. The borders are determined by a 5-bp target site duplication (TSD). The element is inserted into an A/T-rich host sequence that provides putative promoter elements (TATA boxes 1 and 2).
