Arabidopsis thaliana vs Selaginella moellendorffii LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Selaginella moellendorffii (Selaginella moellendorffii, v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 102,032

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

Uncovered: 100,375,332 out of 119,667,750
Covered: 19,292,418 out of 119,667,750

Uncovered: 19,641,818 out of 33,775,569
Matches: 8,810,372 out of 33,775,569
Mismatches: 4,921,811 out of 33,775,569
Insertions: 401,568 out of 33,775,569

Selaginella moellendorffii

Uncovered: 183,883,906 out of 212,645,483
Covered: 28,761,577 out of 212,645,483

Uncovered: 22,828,761 out of 41,155,148
Matches: 11,457,830 out of 41,155,148
Mismatches: 6,481,703 out of 41,155,148
Insertions: 386,854 out of 41,155,148

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

Arabidopsis thaliana Selaginella moellendorffii
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}