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Human vs Orangutan LastZ alignments

Human (Homo sapiens, GRCh37) and Orangutan (Pongo abelii, PPYG2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 66. Human was used as the reference species. After running LastZ , the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Full list of pairwise alignments

Configuration parameters

Gap open penalty (O) 400
Gap extend penalty (E) 30
HSP threshold (K) 5000
Threshold for gapped extension (L) 5000
Threshold for alignments between gapped alignment blocks (H) 3000
Masking count (M) 10
Seed and Transition value (T) 1
Scoring matrix (Q)
A C G T
90 -330 -236 -356
-330 100 -318 -236
-236 -318 100 -330
-356 -236 -330 90

Results

Number of alignment blocks: 548320

Genome coverage(bp) Coding exon coverage (bp)
Human
2,648,804,974 out of 3,098,825,702 34,234,104 out of 35,155,918
Orangutan
2,568,389,383 out of 3,446,771,396 29,328,319 out of 29,861,178