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Table 1 The orientation of AT insertions identified by iPCR and sequencing as reported by Genome ARTIST

From: Genome ARTIST: a robust, high-accuracy aligner tool for mapping transposon insertions and self-insertions

Arrows’ sense The relative orientation of the AT insertion
rb or br Type I orientation. When both arrows are pointing to the same sense and the red arrow (←r or r→) is the closest one relative to an imaginary target point, it means that the junction was sequenced at the 5′ end of the transposon. The variant on the left stands for sequencing with a primer facing towards the 5′ TIR (such as Sp1 for P{lacW}) and the variant on the right stands for sequencing with a primer facing towards the restriction site sequence (such as Plac4 for P{lacW}).
rb→ or ←br Type I orientation. When both arrows are pointing to the same sense and the blue arrow (←b or b→) is the closest one relative to an imaginary target point, it means that the junction was sequenced at the 3′ end of the transposon. The variant on the left stands for sequencing with a primer facing towards the 3′ TIR (such as Spep1 for P{lacW}) and the variant on the right stands for sequencing with a primer facing towards the restriction site sequence (such as Sp6 for P{lacW}).
r b→ or ←b r Type II orientation. When the blue and red arrows are pointing away from each other (a divergence of the senses), it means that the junction was sequenced at the 5′ end of the transposon. The variant on the left stands for sequencing with a primer facing towards the 5′ TIR (such as Sp1 for P{lacW}) and the variant on the right stands for sequencing with a primer facing towards the restriction site sequence (such as Plac4 for P{lacW}).
r→←b or b→←r Type II orientation. When the blue and red arrows are pointing to each other (a convergence of the senses), it means that the junction was sequenced at the 3′ end of the transposon. The variant on the left stands for sequencing with a primer facing towards the 3′ TIR (such as Spep1 for P{lacW}) and the variant on the right stands for sequencing with a primer facing towards the restriction site sequence (such as Sp6 for P{lacW}).
  1. The arrows associated with the genomic and transposon rectangles from the result panel have several possible arrangements that are illustrative for two types of orientation: type I and type II, respectively. In the figure, the superscript letter b stands for the tail of the arrow inside the blue genomic rectangle and letter r marks the tail of the arrow inside the red transposon rectangle which contains the terminal nucleotide (or the TIR). For example, the alignment for the query sequence of P{lacW} insertion in lama (Fig. 2) fits the code ←br. Hence, the insertion is in type I orientation and the AT-genomic junction was sequenced at the 3′ end of the transposon, with a primer facing towards the genomic sequence