Arabidopsis thaliana vs Arabidopsis lyrata BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) were aligned using the BlastZ alignment algorithm ( Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9 ) in Ensembl Plants release 76. Arabidopsis thaliana was used as the reference species. After running BlastZ, the raw BlastZ 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: 107,402

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

Uncovered: 23,241,610 out of 119,667,750
Covered: 96,426,140 out of 119,667,750

Uncovered: 409,274 out of 33,462,323
Matches: 30,753,400 out of 33,462,323
Mismatches: 2,084,121 out of 33,462,323
Insertions: 215,528 out of 33,462,323

Arabidopsis lyrata subsp. lyrata

Uncovered: 117,097,245 out of 206,667,935
Covered: 89,570,690 out of 206,667,935

Uncovered: 5,709,599 out of 35,389,059
Matches: 27,847,408 out of 35,389,059
Mismatches: 1,661,228 out of 35,389,059
Insertions: 170,824 out of 35,389,059

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)