Figure 5

L1 5' inversion structures. For each 5' inverted L1 element for which TSDs were found, the structure at the junction between the two L1 segments was analyzed. Arrows represent the orientation of L1 segments in the genome; an unrearranged L1 would consist of two tandem arrows. Vertical dotted lines indicate breakpoints in the L1 sequence and the alignment of the L1 segments on the genomic sequence. (a) The annotation of the two segments may result in a slight overlap or gap in the contig sequence. Alternatively, the genomic contig sequence may be flawless at the junction of the two fragments. The numbers on the figure for the flawless junction represent the median relative lengths of all of the 5' inverted and 3' direct segments. For those cases in which the 3' direct segment is longer than the 5' inverted segment, the median ratio was 2.3 (70% of cases). (b) In the L1 sequence itself, the two segments that make up the inverted element may overlap (iii) or suggest a small deletion in the L1 sequence (ii). 'X' represents any coordinate in the L1 sequence.