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Human vs tasmanian devil LastZ alignments

Human (Homo sapiens, GRCh37) and tasmanian devil (Sarcophilus harrisii, DEVIL7.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 64. 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) 2200
Threshold for alignments between gapped alignment blocks (H) 2000
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default

Results

Number of alignment blocks: 579816

Genome coverage(bp) Coding exon coverage (bp)
Human
230,833,430 out of 3,098,825,702 30,366,167 out of 35,483,623
tasmanian devil
212,567,312 out of 3,174,693,010 25,035,283 out of 29,265,941