Arabidopsis thaliana vs Oryza sativa Indica BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) 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: 75,679

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

Uncovered: 94,376,755 out of 119,667,750
Covered: 25,290,995 out of 119,667,750

Uncovered: 14,579,643 out of 33,462,323
Matches: 12,306,851 out of 33,462,323
Mismatches: 6,217,139 out of 33,462,323
Insertions: 358,690 out of 33,462,323

Oryza sativa Indica Group

Uncovered: 409,663,176 out of 427,004,890
Covered: 17,341,714 out of 427,004,890

Uncovered: 33,605,146 out of 45,465,969
Matches: 7,681,828 out of 45,465,969
Mismatches: 3,890,066 out of 45,465,969
Insertions: 288,929 out of 45,465,969

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)