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Zebrafish vs Cod LastZ alignments

Zebrafish (Danio rerio, Zv9) and Cod (Gadus morhua, gadMor1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 65. Zebrafish 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: 297047

Genome coverage(bp) Coding exon coverage (bp)
61,539,380 out of 1,412,464,843 28,952,841 out of 39,233,654
42,311,150 out of 832,114,588 21,198,260 out of 29,438,356