Archive Ensembl HomeArchive Ensembl Home

Dog vs Giant Panda LastZ alignments

Dog (Canis familiaris, BROADD2) and Giant Panda (Ailuropoda melanoleuca, ailMel1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 60. Dog 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: 1784186

Genome coverage(bp) Coding exon coverage (bp)
1,964,410,780 out of 2,531,673,953 30,775,228 out of 31,088,517
Giant Panda
1,918,571,140 out of 2,299,492,210 30,311,763 out of 31,119,599