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Fig. 2 | BMC Bioinformatics

Fig. 2

From: DensityMap: a genome viewer for illustrating the densities of features

Fig. 2

Density map of LINE and LTR retrotransposons and rolling-circle transposons (RC) in D. melanogaster. The command line was: DensityMap.pl -i dmel.gff3 -o te -ty 'LINE = fused;LTR = fused;RC = fused = 10′ -sc 40000 -ba white -str_s 15 -str_w 25 -sp 35 -sh 50 -title “Density Map of Gene, Exon, ncRNA and GC%” -la −15 -ro ceil. The arms of chromosomes 2 and 3 are shown in two annotation files 2 L, 2R and 3 L, 3R. Two density maps were drawn for each chromosome, one for LINE retrotransposon and one for LTR transposon. Tilling windows were 40, 000 bp long. The densities of LTR or LINE are shown as a blue- red gradient with 10 % intervals. Zero % RC is shown in grey. Densities of 1 to 9 % are shown in dark blue to red, and those over 10 % are in dark red. The scale is in Mbp

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