Arabidopsis thaliana vs Chlamydomonas reinhardtii BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, v3.1) 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: 13,473

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

Uncovered: 117,873,056 out of 119,667,750
Covered: 1,794,694 out of 119,667,750

Uncovered: 31,811,851 out of 33,462,323
Matches: 1,087,809 out of 33,462,323
Mismatches: 547,088 out of 33,462,323
Insertions: 15,575 out of 33,462,323

Chlamydomonas reinhardtii

Uncovered: 119,449,616 out of 120,404,952
Covered: 955,336 out of 120,404,952

Uncovered: 18,855,804 out of 19,668,972
Matches: 532,519 out of 19,668,972
Mismatches: 273,076 out of 19,668,972
Insertions: 7,573 out of 19,668,972

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)