Ensembl resources are currently in reduced functionality mode. Please see our blog post for the latest information and our Twitter feed

Arabidopsis thaliana vs Vitis vinifera LastZ Results

Back to all analyses

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vitis vinifera (Vitis vinifera, 12X) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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.


Number of alignment blocks: 157,480

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 84,605,119 out of 119,667,750
Covered: 35,062,631 out of 119,667,750

Uncovered: 8,073,411 out of 33,775,569
Matches: 17,538,889 out of 33,775,569
Mismatches: 7,629,060 out of 33,775,569
Insertions: 534,209 out of 33,775,569

Vitis vinifera

Uncovered: 444,212,636 out of 486,265,422
Covered: 42,052,786 out of 486,265,422

Uncovered: 7,863,123 out of 32,794,161
Matches: 16,837,656 out of 32,794,161
Mismatches: 7,471,837 out of 32,794,161
Insertions: 621,545 out of 32,794,161

Configuration parameters

Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Vitis vinifera
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}