Sequence output. The element model shown in green (in A) defragmented three regions of human chromosome Y homologous to segments of the reference sequence of the DNA transposon family MER58B (CHESHIRE_B), shown in B. Hits marked 1 and 2 (in A) are separated on the chromosome by only 26 bp, but in the output model sequence (shown in C) their respective sequences are separated by an internal gap of length 79 – this is the distance along the reference MER58B separating its segments that are aligned to hits 1 and 2. In contrast, the sequences of hits 2 and 3 are output contiguously (without an intervening gap) because they match contiguous segments of MER58B – even though the corresponding chromosomal regions are separated by an ALU SX SINE insertion (blue box above the green model in A). The terminal gap in the model sequence is added to indicate that the annotated alignment of hit 3 ends five nucleotide positions short of the 5' terminus of the MER58B sequence.