Arabidopsis thaliana vs Sorghum bicolor BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Sorghum bicolor (Sorghum bicolor, Sorbi1) 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: 80,370

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

Uncovered: 93,041,557 out of 119,667,750
Covered: 26,626,193 out of 119,667,750

Uncovered: 13,509,289 out of 33,462,323
Matches: 13,002,931 out of 33,462,323
Mismatches: 6,575,316 out of 33,462,323
Insertions: 374,787 out of 33,462,323

Sorghum bicolor

Uncovered: 719,798,397 out of 738,540,932
Covered: 18,742,535 out of 738,540,932

Uncovered: 27,138,911 out of 40,003,363
Matches: 8,335,952 out of 40,003,363
Mismatches: 4,217,871 out of 40,003,363
Insertions: 310,629 out of 40,003,363

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)