Arabidopsis thaliana vs Brachypodium distachyon BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brachypodium distachyon (Brachypodium distachyon, v1.0) 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: 78,420

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

Uncovered: 93,274,691 out of 119,667,750
Covered: 26,393,059 out of 119,667,750

Uncovered: 13,666,668 out of 33,462,323
Matches: 12,895,636 out of 33,462,323
Mismatches: 6,523,871 out of 33,462,323
Insertions: 376,148 out of 33,462,323

Brachypodium distachyon

Uncovered: 253,288,983 out of 271,923,306
Covered: 18,634,323 out of 271,923,306

Uncovered: 21,032,452 out of 34,177,820
Matches: 8,520,833 out of 34,177,820
Mismatches: 4,303,644 out of 34,177,820
Insertions: 320,891 out of 34,177,820

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)