Sequences recovered from the pool of viruses derived from libraries with randomized bases in the U5-IR stem and loop. Panel A: Sequences of the U5-IR stem were randomized as described in Figure 1A. 1st Inf. refers to the sequence pool recovered after the first round of infection with virus derived from the transfected cells. 2nd and 3rd Inf. refers to the sequence pool recovered after the second and third rounds of infections, respectively. Viral DNA was recovered from cells and sequencing was carried out as described in Methods. Panel B: The sequences of the U5-IR loop and stem were randomized as described in Figure 1B. All other notations were as described in legend to panel A, except that 5 rounds of infection were carried out. Rounds 1, 3, and 5 are only shown.