Solanum lycopersicum vs Cynara cardunculus LastZ Results

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Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Cynara cardunculus (Cynara cardunculus var. scolymus, CcrdV1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Solanum lycopersicum 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: 253,671

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum

Uncovered: 769,921,760 out of 827,747,456
Covered: 57,825,696 out of 827,747,456

Uncovered: 8,883,490 out of 36,416,191
Matches: 18,804,957 out of 36,416,191
Mismatches: 8,081,766 out of 36,416,191
Insertions: 645,978 out of 36,416,191

Cynara cardunculus var. scolymus

Uncovered: 660,464,217 out of 724,667,265
Covered: 64,203,048 out of 724,667,265

Uncovered: 5,291,578 out of 32,068,562
Matches: 18,432,607 out of 32,068,562
Mismatches: 7,764,969 out of 32,068,562
Insertions: 579,408 out of 32,068,562

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

Solanum lycopersicum Cynara cardunculus
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}