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Medaka vs Stickleback BlastZ alignments

Medaka (Oryzias latipes, MEDAKA1) and Stickleback (Gasterosteus aculeatus, BROADS1) 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 41. Medaka 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: 401,533

Genome coverage (bp) Coding exon coverage (bp)
Oryzias latipes

Uncovered: 710,417,623 out of 868,983,502
Covered: 158,565,879 out of 868,983,502

Uncovered: 2,077,275 out of 30,193,605
Matches: 22,269,611 out of 30,193,605
Mismatches: 5,609,259 out of 30,193,605
Insertions: 237,460 out of 30,193,605

Gasterosteus aculeatus

Uncovered: 329,966,661 out of 461,533,448
Covered: 131,566,787 out of 461,533,448

Uncovered: 3,832,031 out of 32,649,418
Matches: 22,810,886 out of 32,649,418
Mismatches: 5,669,822 out of 32,649,418
Insertions: 336,679 out of 32,649,418