Alignment of DNA sequences of clones from rounds 4, 5, 6, and 7 of the selection, relative to the undeleted parent sequence, 163.1. Seven constant sequence regions form stems I–VI and are color-coded to correspond with Fig. 4. The five variable regions (R1–R5) show higher frequencies of deletion each successive round (Fig. 7). R3 and R5 appear to converge to particular sequences, whereas R2 and R4 show little sequence preference. A conserved motif at the 3′ end of R1, as well as interactions between the 3′ end of R3 and the 5′ end of R5, are evident in the round 7 sequence data. All isolates from this selection experiment are named as da.x.y, where x is the round, and y is the isolate.
