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Human vs Tasmanian devil LastZ alignments

Human (Homo sapiens, GRCh37) and Tasmanian devil (Sarcophilus harrisii, DEVIL7.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 64. 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.

Configuration parameters

ParameterValue
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:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

Human Tasmanian devil
Chunk size 10,000,000 10,010,000
Overlap 0 10,000
Group set size 10,010,000 10,010,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 579,816

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 2,867,992,272 out of 3,098,825,702
Covered: 230,833,430 out of 3,098,825,702

Uncovered: 5,151,733 out of 35,313,516
Matches: 23,298,710 out of 35,313,516
Mismatches: 6,544,635 out of 35,313,516
Insertions: 318,438 out of 35,313,516

Sarcophilus harrisii

Uncovered: 2,962,125,698 out of 3,174,693,010
Covered: 212,567,312 out of 3,174,693,010

Uncovered: 4,242,179 out of 29,277,268
Matches: 19,521,675 out of 29,277,268
Mismatches: 5,253,970 out of 29,277,268
Insertions: 259,444 out of 29,277,268