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Arabidopsis thaliana vs Physcomitrella patens LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Physcomitrella patens (Physcomitrella patens, Phypa_V3) 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: 99,594

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

Uncovered: 102,984,981 out of 119,667,750
Covered: 16,682,769 out of 119,667,750

Uncovered: 21,129,684 out of 33,775,569
Matches: 8,050,366 out of 33,775,569
Mismatches: 4,359,729 out of 33,775,569
Insertions: 235,790 out of 33,775,569

Physcomitrella patens

Uncovered: 453,209,731 out of 471,852,792
Covered: 18,643,061 out of 471,852,792

Uncovered: 21,436,115 out of 34,318,961
Matches: 8,249,952 out of 34,318,961
Mismatches: 4,346,640 out of 34,318,961
Insertions: 286,254 out of 34,318,961

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 Physcomitrella patens
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}