Fig. 1

Transposition of retrotransposon Tos17 and new sequences in NGS short reads due to the transposition. a Tos17 indicated with head and tail sequences (20 bases in blue) is transposed into the target site (red) of genome sequence (black). b After the integration of Tos17, five base of target site is duplicated at ends of the head and tail sequences. c Because Tos17 was inserted into different positions of genome in ttm2 and ttm5, TSD sequences flanking the head and tail sequence of Tos17 should be different between ttm2 and ttm5. d Detection of junctions in 40 base sequences. Values following sequence are chromosome, position, and direction of first 20 base, and chromosome, position, and direction of last 20 base. TSD method: 25 base (20 base head or tail plus TSD length) sequences are sliced from fastq short reads in each position. Sliced 25 base sequences are paired with same TSD sequence (red) and the grouped with head and tail sequences (blue). If the types of TSD are different between ttm2 and ttm5, the head and tail sequence pair must be ends of TE (panel c). Junction method: 20 base length flanking sequences (black) including TSD (red) and adjacent 20 base length candidates of TE head or tail sequence in panel b are mapped to reference genome sequence (panel d). Map positions of first and adjacent 20 base sequences of all sliced 40 base sequences from fastq short reads are obtained. If adjacent 20 base (blue) is mapped to different position on the reference genome sequence, the adjacent sequence may be a head or tail sequence of TE. Select head and tail pair mapped by flanking sequences to different positions on the reference sequence within and between ttm2 and ttm5. The position of head junction in ttm2 is 22530988 + 20 − 1 = 22531007