Arabidopsis thaliana vs Theobroma cacao LastZ Results

Back to all analyses

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Theobroma cacao (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. 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: 113,213

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

Uncovered: 76,512,904 out of 119,667,750
Covered: 43,154,846 out of 119,667,750

Uncovered: 6,049,246 out of 33,462,323
Matches: 18,916,999 out of 33,462,323
Mismatches: 7,943,057 out of 33,462,323
Insertions: 553,021 out of 33,462,323

Theobroma cacao

Uncovered: 315,280,302 out of 345,993,675
Covered: 30,713,373 out of 345,993,675

Uncovered: 15,444,308 out of 34,800,751
Matches: 13,314,975 out of 34,800,751
Mismatches: 5,477,226 out of 34,800,751
Insertions: 564,242 out of 34,800,751

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Theobroma cacao
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}