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Arabidopsis thaliana vs Ipomoea triloba LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) 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: 151,803

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

Uncovered: 84,807,217 out of 119,667,750
Covered: 34,860,533 out of 119,667,750

Uncovered: 9,343,071 out of 33,775,569
Matches: 16,252,093 out of 33,775,569
Mismatches: 7,630,877 out of 33,775,569
Insertions: 549,528 out of 33,775,569

Ipomoea triloba

Uncovered: 416,608,013 out of 461,827,428
Covered: 45,219,415 out of 461,827,428

Uncovered: 11,888,605 out of 39,533,495
Matches: 18,379,559 out of 39,533,495
Mismatches: 8,536,069 out of 39,533,495
Insertions: 729,262 out of 39,533,495

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 Ipomoea triloba
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}