Theobroma cacao vs Citrus clementina LastZ Results

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Theobroma cacao (Theobroma cacao, Criollo_cocoa_genome_V2) and Citrus clementina (Citrus clementina, Citrus_clementina_v1.0) 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: 159,581

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

Uncovered: 266,710,133 out of 324,719,311
Covered: 58,009,178 out of 324,719,311

Uncovered: 2,644,240 out of 29,183,654
Matches: 19,645,491 out of 29,183,654
Mismatches: 6,395,911 out of 29,183,654
Insertions: 498,012 out of 29,183,654

Citrus clementina

Uncovered: 232,558,279 out of 301,364,702
Covered: 68,806,423 out of 301,364,702

Uncovered: 2,360,759 out of 30,721,724
Matches: 20,883,355 out of 30,721,724
Mismatches: 6,928,535 out of 30,721,724
Insertions: 549,075 out of 30,721,724

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 Citrus clementina
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}