Human vs Marmoset BlastZ alignments

Human (Homo sapiens, GRCh37) and Marmoset (Callithrix jacchus, C_jacchus3.2.1) 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 59. 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) 2200
Threshold for alignments between gapped alignment blocks (H) 2000
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default

Results

Number of alignment blocks: 1772373

Genome coverage(bp) Coding exon coverage (bp)
Human
1,859,664,671 out of 3,098,825,702 34,691,943 out of 35,483,623
Marmoset
1,765,981,000 out of 2,933,982,654 31,725,356 out of 33,717,870