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Human vs Giant Panda LastZ alignments

Human (Homo sapiens, GRCh37) and Giant Panda (Ailuropoda melanoleuca, ailMel1) 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: 2018327

Genome coverage(bp) Coding exon coverage (bp)
Human
1,584,612,089 out of 3,098,825,702 34,296,680 out of 35,483,623
Giant Panda
1,497,681,881 out of 2,299,492,210 30,151,759 out of 31,119,599