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Human vs Lesser hedgehog tenrec BlastZ alignments

Human (Homo sapiens, GRCh37) and Lesser hedgehog tenrec (Echinops telfairi, TENREC) 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 release 55. Human 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.

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

Results

Number of alignment blocks: 1,377,395

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 2,389,140,502 out of 3,098,825,702
Covered: 709,685,200 out of 3,098,825,702

Uncovered: 6,397,923 out of 35,313,516
Matches: 23,608,950 out of 35,313,516
Mismatches: 4,925,948 out of 35,313,516
Insertions: 380,695 out of 35,313,516

Echinops telfairi

Uncovered: 3,181,481,054 out of 3,833,568,392
Covered: 652,087,338 out of 3,833,568,392

Uncovered: 5,094,090 out of 25,951,720
Matches: 17,677,165 out of 25,951,720
Mismatches: 3,112,311 out of 25,951,720
Insertions: 68,154 out of 25,951,720