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Arabidopsis thaliana vs Arabidopsis lyrata LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) 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: 192,580

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

Uncovered: 25,251,033 out of 119,667,750
Covered: 94,416,717 out of 119,667,750

Uncovered: 587,653 out of 33,775,569
Matches: 30,840,254 out of 33,775,569
Mismatches: 2,113,224 out of 33,775,569
Insertions: 234,438 out of 33,775,569

Arabidopsis lyrata subsp. lyrata

Uncovered: 91,565,566 out of 206,667,935
Covered: 115,102,369 out of 206,667,935

Uncovered: 1,189,109 out of 35,389,059
Matches: 31,533,841 out of 35,389,059
Mismatches: 2,402,447 out of 35,389,059
Insertions: 263,662 out of 35,389,059

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 Arabidopsis lyrata
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}