Figure 1

Criteria for rejecting related sequence downstream from another L1 in the genome. At the top of the figure is a schematic of an L1-TD. The red segment represents a 3'-transduced sequence; in (a-f), the red segment represents a possible BLAST hit with a sequence downstream of another L1 element. When searching for the master element that gave rise to the transduced sequence, the following scenarios must not be true: (a) two different but nearly adjacent L1s share the same 3 kb flanking sequence; (b) the sequence shares less than 90% identity with the transduced sequence; (c) the length of the match is less than 30% of the transduced sequence; (d) the match is in the opposite orientation with respect to the L1 sequence; (e) the position of the match with respect to the end of the L1 differs by more than 20 nucleotides; (f) the two genomic segments are duplications and the alignment extends past the TSD. The percentages shown below criteria (a-e) indicate the frequency of finding the depicted structure in our entire collection of L1-TDs (and thus rejecting a candidate on that basis).