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.
Phillippy et al. Genome Biology 2008 9:R55 doi:10.1186/gb-2008-9-3-r55