Arabidopsis thaliana vs Cyanidioschyzon merolae LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cyanidioschyzon merolae (Cyanidioschyzon merolae strain 10D, ASM9120v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Arabidopsis thaliana 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: 6,297

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 118,271,128 out of 119,667,750
Covered: 1,396,622 out of 119,667,750

Uncovered: 32,479,085 out of 33,775,569
Matches: 806,221 out of 33,775,569
Mismatches: 459,755 out of 33,775,569
Insertions: 30,508 out of 33,775,569

Cyanidioschyzon merolae strain 10D

Uncovered: 16,066,082 out of 16,728,945
Covered: 662,863 out of 16,728,945

Uncovered: 6,843,905 out of 7,493,795
Matches: 402,788 out of 7,493,795
Mismatches: 233,199 out of 7,493,795
Insertions: 13,903 out of 7,493,795

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)