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 alignmentsGap 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) | |
---|---|---|
Dog | ![]() |
![]() |
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 |