Theobroma cacao vs Arabidopsis halleri LastZ Results

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Theobroma cacao (Theobroma cacao, Theobroma_cacao_20110822) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) 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: 132,539

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

Uncovered: 308,296,121 out of 345,993,675
Covered: 37,697,554 out of 345,993,675

Uncovered: 10,604,166 out of 34,800,751
Matches: 16,280,494 out of 34,800,751
Mismatches: 7,231,116 out of 34,800,751
Insertions: 684,975 out of 34,800,751

Arabidopsis halleri subsp. gemmifera

Uncovered: 154,404,348 out of 196,243,198
Covered: 41,838,850 out of 196,243,198

Uncovered: 11,396,155 out of 38,698,211
Matches: 18,802,101 out of 38,698,211
Mismatches: 7,951,045 out of 38,698,211
Insertions: 548,910 out of 38,698,211

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 Arabidopsis halleri
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}