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Human vs Cow LastZ alignments

Human (Homo sapiens, GRCh37) and Cow (Bos taurus, UMD3.1) 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) 3000
Threshold for alignments between gapped alignment blocks (H) 2200
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default


Number of alignment blocks: 2240708

Genome coverage(bp) Coding exon coverage (bp)
1,400,606,471 out of 3,098,825,702 34,463,838 out of 35,483,623
1,322,460,687 out of 2,670,422,299 30,460,957 out of 32,345,388