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Opossum vs tasmanian devil LastZ alignments

Opossum (Monodelphis domestica, BROADO5) and tasmanian devil (Sarcophilus harrisii, DEVIL7.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 64. Opossum 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) 2200
Threshold for alignments between gapped alignment blocks (H) 2000
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default

Results

Number of alignment blocks: 2775298

Genome coverage(bp) Coding exon coverage (bp)
Opossum
1,703,326,007 out of 3,605,631,728 30,251,863 out of 31,790,129
tasmanian devil
1,587,580,726 out of 3,174,693,010 26,901,050 out of 29,265,941