Arabidopsis thaliana vs Cucumis melo LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cucumis melo (Cucumis melo, Melonv4) 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.

Results

Number of alignment blocks: 123,091

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

Uncovered: 85,871,551 out of 119,667,750
Covered: 33,796,199 out of 119,667,750

Uncovered: 9,517,873 out of 33,775,569
Matches: 16,391,268 out of 33,775,569
Mismatches: 7,353,695 out of 33,775,569
Insertions: 512,733 out of 33,775,569

Cucumis melo

Uncovered: 324,670,055 out of 357,857,370
Covered: 33,187,315 out of 357,857,370

Uncovered: 8,025,206 out of 27,459,425
Matches: 13,039,335 out of 27,459,425
Mismatches: 5,859,188 out of 27,459,425
Insertions: 535,696 out of 27,459,425

Configuration parameters

ParameterValue
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)
Default:
     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 Cucumis melo
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options