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Human vs Shrew BlastZ alignments

Human (Homo sapiens, GRCh37) and Shrew (Sorex araneus, COMMON_SHREW1) 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

Results

Number of alignment blocks: 1229844

Genome coverage(bp) Coding exon coverage (bp)
Human
633,411,317 out of 3,098,825,702 26,378,376 out of 35,483,623
Shrew
580,691,524 out of 2,944,193,050 16,857,482 out of 20,841,358