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 »

Triticum aestivum vs Oryza sativa Japonica Group LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Triticum aestivum 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
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

ParameterTriticum aestivumOryza sativa Japonica Group
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 1,354,149 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 13,961,074,617 out of 14,547,261,565
Covered: 586,186,948 out of 14,547,261,565

Uncovered: 10,484,082 out of 133,674,966
Matches: 95,201,156 out of 133,674,966
Mismatches: 25,241,212 out of 133,674,966
Insertions: 2,748,516 out of 133,674,966
Identity over aligned base-pairs: 77.3%

Oryza sativa Japonica Group

Uncovered: 278,641,612 out of 375,049,285
Covered: 96,407,673 out of 375,049,285

Uncovered: 2,739,124 out of 34,818,902
Matches: 24,707,783 out of 34,818,902
Mismatches: 6,448,396 out of 34,818,902
Insertions: 923,599 out of 34,818,902
Identity over aligned base-pairs: 77.0%

Block size distribution

Size range All 1,354,149 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,246
39.6 kb
10 bp - 100 bp
235,789
15.4 Mb
148,502
10.0 Mb
100 bp - 1 kb
937,698
332.0 Mb
525,909
175.7 Mb
1 kb - 10 kb
173,404
301.4 Mb
170,647
404.1 Mb
10 kb - 100 kb
12
146.2 kb
3,821
58.7 Mb
100 kb - 1 Mb
4
439.2 kb