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Human vs Hedgehog BlastZ alignments

Human (Homo sapiens, GRCh37) and Hedgehog (Erinaceus europaeus, HEDGEHOG) 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.

Full list of pairwise alignments

Configuration parameters

Gap open penalty (O) 400
Gap extend penalty (E) 30
HSP threshold (K) 3000
Threshold for gapped extension (L) 3000
Threshold for alignments between gapped alignment blocks (H) 2200
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default


Number of alignment blocks: 1278795

Genome coverage(bp) Coding exon coverage (bp)
612,039,263 out of 3,098,825,702 28,308,898 out of 35,483,623
559,094,190 out of 3,377,524,115 19,374,961 out of 23,708,111