Theobroma cacao vs Arabidopsis halleri LastZ Results

Back to all analyses

Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) 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: 132,426

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

Uncovered: 287,144,121 out of 324,719,311
Covered: 37,575,190 out of 324,719,311

Uncovered: 6,232,841 out of 29,183,654
Matches: 15,505,984 out of 29,183,654
Mismatches: 6,811,218 out of 29,183,654
Insertions: 633,611 out of 29,183,654

Arabidopsis halleri subsp. gemmifera

Uncovered: 154,442,015 out of 196,243,198
Covered: 41,801,183 out of 196,243,198

Uncovered: 11,399,026 out of 38,698,211
Matches: 18,821,458 out of 38,698,211
Mismatches: 7,929,224 out of 38,698,211
Insertions: 548,503 out of 38,698,211

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 Arabidopsis halleri
Chunk size 10,100,000 10,100,000
Overlap 100,000 100,000
Group set size 10,100,000 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}