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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.

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

Opossum 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} {default_soft_masking => 1}

Results

Number of alignment blocks: 2,775,298

Genome coverage (bp) Coding exon coverage (bp)
Monodelphis domestica

Uncovered: 1,902,305,721 out of 3,605,631,728
Covered: 1,703,326,007 out of 3,605,631,728

Uncovered: 2,900,988 out of 33,971,162
Matches: 27,110,258 out of 33,971,162
Mismatches: 3,760,657 out of 33,971,162
Insertions: 199,259 out of 33,971,162

Sarcophilus harrisii

Uncovered: 1,587,112,284 out of 3,174,693,010
Covered: 1,587,580,726 out of 3,174,693,010

Uncovered: 2,377,321 out of 29,277,268
Matches: 23,736,397 out of 29,277,268
Mismatches: 3,003,308 out of 29,277,268
Insertions: 160,242 out of 29,277,268