makeblastdb -in mt.fasta -dbtype nucl -out mt
blastn -query cp.fasta -db mt -outfmt 6 > output.txt

df<-data.frame(chr=c(rep("chloroplast",2),rep("mitochondrial",2)),x=c(1,131478,1,444567),y=c(0,1,0,1))> dfchr      x y
1   chloroplast      1 0
2   chloroplast 131478 1
3 mitochondrial      1 0
4 mitochondrial 444567 1

df1<-read.csv("output6.txt",stringsAsFactors = F,header=F,sep="t")

library(circlize)
library(RColorBrewer)
library(ComplexHeatmap)
col<-RColorBrewer::brewer.pal(6,"Paired")
circos.par("start.degree" = 130)
circos.initialize(factors = df$chr,x=df$x)
circos.trackPlotRegion(factors = df$chr,y=df$y,panel.fun = function(x,y){circos.axis()},track.height = 0.1)
highlight.sector(sector.index = "chloroplast",col=col[1])
highlight.sector(sector.index = "mitochondrial",col=col[2])
circos.text(x=70000,y=0.5,labels = "chloroplast",sector.index = "chloroplast")
circos.text(x=220000,y=0.5,labels = "mitochondrial",sector.index = "mitochondrial",facing = "outside")
col_fun = colorRamp2(c(70,90,100),c("green", "yellow", "red"))
for (i in 1:13){x<-sort(c(df1[i,8],df1[i,7]))y<-sort(c(df1[i,10],df1[i,9]))z<-df1[i,3]circos.link("chloroplast",x,"mitochondrial",y,col=add_transparency(col_fun(z)))
}
circos.clear()
lgd_links = Legend(at = c(70, 80, 90, 100), col_fun = col_fun, title_position = "topleft",title = "identity(%)")
lgd_list_vertical = packLegend(lgd_links)draw(lgd_list_vertical, x = unit(10, "mm"), y = unit(10, "mm"), just = c("left", "bottom"))

circos.par("start.degree" = 130)

circos.trackPlotRegion(factors = df$chr,y=df$y,panel.fun = function(x,y){circos.axis()},track.height = 0.1)