Medicago truncatula vs Theobroma cacao LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Theobroma cacao (Theobroma cacao, Theobroma_cacao_20110822) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula 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: 168,676

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 355,953,210 out of 412,800,391
Covered: 56,847,181 out of 412,800,391

Uncovered: 15,189,671 out of 50,132,764
Matches: 24,263,320 out of 50,132,764
Mismatches: 9,975,025 out of 50,132,764
Insertions: 704,748 out of 50,132,764

Theobroma cacao

Uncovered: 301,073,295 out of 345,993,675
Covered: 44,920,380 out of 345,993,675

Uncovered: 8,672,536 out of 34,800,751
Matches: 18,009,022 out of 34,800,751
Mismatches: 7,476,417 out of 34,800,751
Insertions: 642,776 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

Medicago truncatula Theobroma cacao
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}