Theobroma cacao vs Corchorus capsularis LastZ Results

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Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Corchorus capsularis (Corchorus capsularis, CCACVL1_1.0) 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: 183,973

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

Uncovered: 224,995,741 out of 324,719,311
Covered: 99,723,570 out of 324,719,311

Uncovered: 1,300,652 out of 29,183,654
Matches: 23,792,300 out of 29,183,654
Mismatches: 3,768,474 out of 29,183,654
Insertions: 322,228 out of 29,183,654

Corchorus capsularis

Uncovered: 214,520,787 out of 317,178,409
Covered: 102,657,622 out of 317,178,409

Uncovered: 3,542,435 out of 30,371,305
Matches: 22,712,617 out of 30,371,305
Mismatches: 3,718,663 out of 30,371,305
Insertions: 397,590 out of 30,371,305

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 Corchorus capsularis
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}