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Opossum vs Wallaby BlastZ alignments

Opossum (Monodelphis domestica, BROADO5) and Wallaby (Macropus eugenii, Meug_1.0) were aligned using the BlastZ alignment algorithm ( Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9 ) in Ensembl release 57. Opossum was used as the reference species. After running BlastZ, the raw BlastZ 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Results

Number of alignment blocks: 2,212,804

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

Uncovered: 2,240,901,513 out of 3,605,631,728
Covered: 1,364,730,215 out of 3,605,631,728

Uncovered: 5,501,859 out of 33,971,162
Matches: 24,736,225 out of 33,971,162
Mismatches: 3,538,677 out of 33,971,162
Insertions: 194,401 out of 33,971,162

Macropus eugenii

Uncovered: 1,667,774,192 out of 2,955,773,937
Covered: 1,287,999,745 out of 2,955,773,937

Uncovered: 5,256,765 out of 25,589,509
Matches: 18,265,977 out of 25,589,509
Mismatches: 1,994,592 out of 25,589,509
Insertions: 72,175 out of 25,589,509