Fig. 3

Sequence alignment of mutations. The top line is the sequence from plasmid pBRCINR including the 5′ sequence and both EcoRI sites. (A) Deletions. The sequence from 38 bp 5′ to the EcoRI site, the inserted sequence, and the 3′ EcoRI site are illustrated. The restriction sites are identified by a line over the sequence. The inverted repeat is identified by the opposing arrows above the sequence. Unpaired bases in the proposed stem-loop structure are white with a black background, and bases across from these unpaired bases are black with a gray background. The hairpin loop is boxed. Arrows are above the inverted repeat sequence. Deletions are aligned beneath by gaps in the sequence. The sequences are referred to by the lowercase letters to the left of the sequences. To the right are the number of times this was identified in the three bacterial strains. Because the clones selected for sequence were representative of mutation types and not every mutation event scored by reversion, this number is not indicative of the total number of times the event occurred. (B) Insertions. The sequence from 38 bp 5′ to the EcoR1 site, the inserted sequence, and the 3′ EcoR1 site are illustrated. The restriction sites are identified by a line over the sequence. The opposing arrows over the sequence depicts the inverted repeat. Unpaired bases in the proposed stem-loop structure are white with a black background, and bases across from these unpaired bases are black with a gray background, while the hairpin loop is boxed. The insertions are depicted in black and their template is illustrated by gray background shading. (C) Complex mutations. The coding is the same as in A and B. The inserts are in black and the templated sequences have gray background shading, while the gaps represent deletions.