Arabidopsis thaliana vs Selaginella moellendorffii BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Selaginella moellendorffii (Selaginella moellendorffii, 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: 50,210

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

Uncovered: 99,805,739 out of 119,667,750
Covered: 19,862,011 out of 119,667,750

Uncovered: 18,799,813 out of 33,462,323
Matches: 9,187,332 out of 33,462,323
Mismatches: 5,094,580 out of 33,462,323
Insertions: 380,598 out of 33,462,323

Selaginella moellendorffii

Uncovered: 200,173,125 out of 212,645,483
Covered: 12,472,358 out of 212,645,483

Uncovered: 32,222,953 out of 41,155,148
Matches: 5,631,160 out of 41,155,148
Mismatches: 3,108,866 out of 41,155,148
Insertions: 192,169 out of 41,155,148

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)