Figure 1.

Misplaced reads caused by the two copy repeat R and leading to (a) unsatisfied mate-pairs and (b) correlated SNPs. Unique sequence is shown in white and repetitive sequence in gray. Example mate-pairs are drawn as connected arrow heads. Properly oriented mates point towards each other, and properly sized pairs are connected with a solid line. All mates can be satisfied and the correlated SNP removed if the bottom two reads in R₁ are moved to R₂.