Theobroma cacao Belizian Criollo B97-61/B2 vs Theobroma cacao Matina 1-6 LastZ Results

Back to all analyses

Theobroma cacao Belizian Criollo B97-61/B2 (Theobroma cacao, Criollo_cocoa_genome_V2) and Theobroma cacao Matina 1-6 (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Theobroma cacao Belizian Criollo B97-61/B2 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: 120,003

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

Uncovered: 7,546,697 out of 324,719,311
Covered: 317,172,614 out of 324,719,311

Uncovered: 47,108 out of 29,183,654
Matches: 28,829,654 out of 29,183,654
Mismatches: 295,550 out of 29,183,654
Insertions: 11,342 out of 29,183,654

Theobroma cacao

Uncovered: 8,211,323 out of 345,993,675
Covered: 337,782,352 out of 345,993,675

Uncovered: 174,978 out of 34,800,751
Matches: 33,856,130 out of 34,800,751
Mismatches: 743,409 out of 34,800,751
Insertions: 26,234 out of 34,800,751

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 Belizian Criollo B97-61/B2 Theobroma cacao Matina 1-6
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options