Arabidopsis thaliana vs Cucumis sativus LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cucumis sativus (Cucumis sativus, ASM407v2) 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: 111,212

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

Uncovered: 86,090,083 out of 119,667,750
Covered: 33,577,667 out of 119,667,750

Uncovered: 9,673,734 out of 33,775,569
Matches: 16,280,672 out of 33,775,569
Mismatches: 7,315,063 out of 33,775,569
Insertions: 506,100 out of 33,775,569

Cucumis sativus

Uncovered: 163,352,304 out of 193,829,320
Covered: 30,477,016 out of 193,829,320

Uncovered: 6,191,625 out of 26,192,424
Matches: 13,428,071 out of 26,192,424
Mismatches: 6,043,108 out of 26,192,424
Insertions: 529,620 out of 26,192,424

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 sativus
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}