Theobroma cacao vs Brassica rapa LastZ Results
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Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Brassica rapa (Brassica rapa, Brapa_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: 191,926
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Theobroma cacao |
Uncovered: 287,522,829 out of 324,719,311 |
Uncovered: 6,400,454 out of 29,183,654 |
Brassica rapa |
Uncovered: 226,356,511 out of 283,822,783 |
Uncovered: 10,984,493 out of 48,055,850 |
Configuration parameters
Parameter | Value |
---|---|
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 rapa | |
---|---|---|
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} |