Percent Identity Plot (PIP) Analysis of Naip Genomic Sequences. The alignments have been generated and drawn as described in Methods. The figure indicates regions for which there are alignments having >50% identity. Before alignment, the genomic sequences were masked by RepeatMasker. Interspersed repeats in the mouse sequence are indicated as follows: (white pointed box) L1; (light gray box) SINE other than MIR; (black box) MIR or LINE2; (dark gray box) all others. Other elements in the sequence are indicated as follows: (arrows), positions and directions of transcription of known genes in the query sequence; (numbered black rectangles) positions of exons within the transcription units; (short gray rectangles), position of CpG islands. The figure shows several PIPs between mouse Naip genes.(A) Comparison of the Naip5 to all the other sequenced Naips, showing the existence of two distinct families of gene loci: Naip1/2/3 and Naip4/5/6/7. (B) Comparison of Naip3 with the ΔNaiploci. The elongated gray boxes inside the PIP panels indicate regions in which a comparison between the two sequences is not possible because one of the sequences ends.