Genome-wide detection of ITR-driven gene modifications. (a) The set of human gene loci within human SDs was retrieved. Each locus is composed of transcripts that overlap on the same strand. (b) After an all-against-all alignment between exons, only loci that share at least one exon with 95% coverage and 90% sequence identity were kept. The alignments could involve complete exons (blue) or portions of adjacent exons (pink). (c) From this dataset, alignments with a variable number of ITR units were extracted. (d) The effect of the variable ITR on the gene structure was manually checked to remove false positives and discriminate between exon and intron modifications.