Sequence assembly alignments to D. melanogaster arm 3R show longer well-assembled scaffolds for the FASSI-1 and FASSI-6 WGAs compared to a control without map-derived constraints at 4× coverage. Scaffolds of all sizes containing at least two contigs, each aligning to the reference genome with 70% sequence identity over the contig length and 90% over the wuBLAST hit length, are displayed. The blue and yellow lines represent contigs of a specific scaffold. The color switch signifies a change in the identity of aligned scaffolds. White spaces indicate regions without suitable contig alignment. The first track shows repeated segments (vertical gray lines) at specified positions on the chromosome. Repeats >500 bp in size and sharing >95% sequence identity are shown on the first track. Tracks 2, 3, and 4 show scaffold alignments between the finished genome and the control assembly, FASSI-1 and FASSI-6, respectively.
