Supplementary Figure 14: Pulse-field gel electrophoresis of RP11-482A22 BAC DNA to determine insert length.

The span of BAC end sequences relative to GRCh38 reference assembly provides estimates of 57 kb to the right of the repeats and 76 kb to the left of the repeats (depicted in black). To determine the length of the repeats, we performed NotI and AatII digests on RP11-482 DNA. The NotI digest isolates the insert DNA in its entirety from the cloning vector insert, pBACe3.6, providing evidence for a cloned insert in the range of 170–175 kb (blue) and an 11.6-kb cloning vector band (red). After subtraction of the known flanking region sizes, this estimate provides a repeat region in the range of 36.7–41.7 kb, or 7.5 to 8.5 copies of the CT47 repeat. The AatII digest was expected to cut the BAC three times, as illustrated in the schematic, providing three resulting fragments: (a) 108 kb including the upstream flanking region (50 kb), the downstream flanking region (46 kb) and the cloning vector insert (11.6 kb), shown in purple; (b) a 23-kb region directly downstream from the repeat array (blue), and a region observed by PFGE to be ≍50 kb that spans the CT47 repeat cluster (providing evidence for a 37-kb repeat region after subtraction of 12 kb of known flanking sequence, marked with gray shading). Regions providing evidence for repeat copy number are highlighted in yellow.