vs BlastZ Results

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(, TAIR10) and (, ASM242v1) 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. 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: 67,210

Genome coverage (bp) Coding exon coverage (bp)

Uncovered: 102,800,451 out of 119,667,750
Covered: 16,867,299 out of 119,667,750

Uncovered: 20,505,494 out of 33,462,323
Matches: 8,283,599 out of 33,462,323
Mismatches: 4,446,370 out of 33,462,323
Insertions: 226,860 out of 33,462,323

Uncovered: 468,558,186 out of 479,985,347
Covered: 11,427,161 out of 479,985,347

Uncovered: 26,987,914 out of 34,827,652
Matches: 5,000,990 out of 34,827,652
Mismatches: 2,648,588 out of 34,827,652
Insertions: 190,160 out of 34,827,652

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)