Theobroma cacao vs Brassica oleracea LastZ Results

Back to all analyses

Theobroma cacao (Theobroma cacao, Theobroma_cacao_20110822) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Theobroma cacao 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: 215,218

Genome coverage (bp) Coding exon coverage (bp)
Theobroma cacao

Uncovered: 307,309,047 out of 345,993,675
Covered: 38,684,628 out of 345,993,675

Uncovered: 10,631,017 out of 34,800,751
Matches: 16,134,007 out of 34,800,751
Mismatches: 7,242,346 out of 34,800,751
Insertions: 793,381 out of 34,800,751

Brassica oleracea var. oleracea

Uncovered: 423,846,736 out of 488,622,507
Covered: 64,775,771 out of 488,622,507

Uncovered: 21,157,591 out of 61,722,508
Matches: 27,846,111 out of 61,722,508
Mismatches: 11,909,583 out of 61,722,508
Insertions: 809,223 out of 61,722,508

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

Theobroma cacao Brassica oleracea
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}