Upcoming Ensembl Platform Transition

This is the final release of its kind on this website.

In summer 2026, this site will bring you to the new Ensembl platform currently at beta.ensembl.org.
Please bookmark this archive to retain access to the current site, tools and functionality until they are available on the new platform -> eg63-plants.ensembl.org

Ensembl Genomes HomeEnsembl Plants HomeEnsembl Plants Home ▼
More ▼
Search »

Oryza meridionalis vs Oryza sativa Japonica Group LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was 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)3000
Threshold for alignments between gapped alignment blocks (H)2200
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

ParameterOryza meridionalisOryza sativa Japonica Group
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}

Statistics over 343,106 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza meridionalis

Uncovered: 97,874,978 out of 335,668,232
Covered: 237,793,254 out of 335,668,232

Uncovered: 420,569 out of 35,224,824
Matches: 33,566,367 out of 35,224,824
Mismatches: 995,076 out of 35,224,824
Insertions: 242,812 out of 35,224,824
Identity over aligned base-pairs: 96.4%

Oryza sativa Japonica Group

Uncovered: 183,806,907 out of 375,049,285
Covered: 191,242,378 out of 375,049,285

Uncovered: 6,100,995 out of 34,818,902
Matches: 27,983,787 out of 34,818,902
Mismatches: 582,076 out of 34,818,902
Insertions: 152,044 out of 34,818,902
Identity over aligned base-pairs: 97.4%

Block size distribution

Size range All 343,106 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4,170
23.8 kb
10 bp - 100 bp
76,724
4.6 Mb
37,948
2.4 Mb
100 bp - 1 kb
202,043
69.7 Mb
88,437
28.3 Mb
1 kb - 10 kb
59,055
154.4 Mb
13,787
30.1 Mb
10 kb - 100 kb
1,114
14.8 Mb
508
12.5 Mb
100 kb - 1 Mb
53
10.5 Mb
1 Mb - 10 Mb
3
24.1 Mb
10 Mb - 100 Mb
9
135.8 Mb