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Human vs Opossum BlastZ alignments

Human (Homo sapiens, GRCh37) and Opossum (Monodelphis domestica, BROADO5) 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) 2200
Threshold for gapped extension (L) 10000
Threshold for alignments between gapped alignment blocks (H) 2000
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q)
A C G T
91 -90 -25 -100
-90 100 -100 -25
-25 -100 100 -90
-100 -25 -90 91

Results

Number of alignment blocks: 742339

Genome coverage(bp) Coding exon coverage (bp)
Human
330,760,207 out of 3,098,825,702 30,622,702 out of 35,483,623
Opossum
304,720,276 out of 3,605,631,728 26,329,960 out of 31,790,129