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Arabidopsis thaliana vs Chlamydomonas reinhardtii LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, Chlamydomonas_reinhardtii_v5.5) 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.


Number of alignment blocks: 13,751

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

Uncovered: 118,025,804 out of 119,667,750
Covered: 1,641,946 out of 119,667,750

Uncovered: 32,241,041 out of 33,775,569
Matches: 1,012,062 out of 33,775,569
Mismatches: 510,244 out of 33,775,569
Insertions: 12,222 out of 33,775,569

Chlamydomonas reinhardtii

Uncovered: 110,094,124 out of 111,098,438
Covered: 1,004,314 out of 111,098,438

Uncovered: 38,241,832 out of 39,157,072
Matches: 599,595 out of 39,157,072
Mismatches: 307,063 out of 39,157,072
Insertions: 8,582 out of 39,157,072

Configuration parameters

Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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)
     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 Chlamydomonas reinhardtii
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}