Figure 1
An example of sequence comparison between two rice lines, Nipponbare and 93-11. The region of 6,070,001–6,629,564 bp on chromosome 11 (based on IRGSP database) is shown. These 683 kb consecutive sequences, sampled around R gene clusters, were aligned between Nipponbare (559,563 bp) and 93-11 (428,114 bp). Dotted line represents where a sequence in one line cannot be aligned with a sequence at the corresponding position in the other line. Genes are shown as square boxes pointing in the direction of transcription. This region contains 70 non-TE genes in Nipponbare and 62 in 93-11. 53 allelic non-TE genes are colored as green, 8 P/A as red, 4 P/Ad as orange, 14 AL as magenta, and 30 TE genes as blue boxes. All R genes are labeled above or below the boxes. The sizes of genes, intergenic sequences, and indels are proportionally scaled down. In this region, the PAG is 30.7%, and the percentage of asymmetric genes is 39.4% ((8 P/A +4 P/Ad +14 AL)/66).