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Human vs Rabbit LastZ alignments

Human (Homo sapiens, GRCh37) and Rabbit (Oryctolagus cuniculus, oryCun2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 60. 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) 3000
Threshold for gapped extension (L) 3000
Threshold for alignments between gapped alignment blocks (H) 2200
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default

Results

Number of alignment blocks: 2036094

Genome coverage(bp) Coding exon coverage (bp)
Human
1,326,966,577 out of 3,098,825,702 32,930,581 out of 35,483,623
Rabbit
1,221,978,809 out of 2,737,473,256 27,856,841 out of 29,950,200