Figure 3.

Breakpoints for the most recent Abp gene duplication. A) The region of alignment in all three sequences between ~30 kb and ~36 kb includes the nearly full-length L1Md_T sequence. The aligned sequences are shown as bars with the L1Md_T element set off by a bracket above the bars. Bar 1: the 33 kb region immediately to the left of Abpbg14p; bar 2: the L1Md_T repeat on the right flank of Abpa15; and bar 3: the region containing the L1Md_T repeat to the right of Abpa17. Bars in the upper part of the figure show the alignment of the three sequences over slightly more than 20 kb. Regions that align in all three sequences are tinted yellow; regions that align in two of three are tinted green and regions that do not align in any of the three are untinted. B) An alignment of 360 bp of the three sequences that surround the gap shown by black arrows in panel A. Two duplications that occur within the gap are depicted with red bars. We bracketed in green a GGTT preceding the rest of the duplication, which is marked with a red bar/bracket. We note that there are also shorter indels, e.g., TGTGTTTTCCTGTTTTTC, within the gap. Proximal to and at four nucleotides in the gap (GGTT), sequences 2 and 3 are identical (i.e. seven of eleven divergent sites shown in the figure). However, distal to the gap, 2 is identical to 1, while 3 differs at four divergent sites. C) Bars representing the entire L1Md_T sequences 1, 2 and 3 show that, for 384 divergent sites proximal to the breakpoint, 2 is identical to 3; for 127 divergent sites following the breakpoint 2 is identical to 1.