Human (Homo sapiens, GRCh37) and Chimpanzee (Pan troglodytes, CHIMP2.1) 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 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 alignmentsGap open penalty (O) | 600 | ||||||||||||||||||||
Gap extend penalty (E) | 150 | ||||||||||||||||||||
HSP threshold (K) | 4500 | ||||||||||||||||||||
Threshold for gapped extension (L) | 2200 | ||||||||||||||||||||
Threshold for alignments between gapped alignment blocks (H) | 2000 | ||||||||||||||||||||
Masking count (M) | 50 | ||||||||||||||||||||
Seed and Transition value (T) | 2 | ||||||||||||||||||||
Scoring matrix (Q) |
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Number of alignment blocks: 692174
Genome coverage(bp) | Coding exon coverage (bp) | |
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Human | ![]() |
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2,263,640,977 out of 3,098,825,702 | 34,385,806 out of 35,483,623 | |
Chimpanzee | ![]() |
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2,220,936,942 out of 3,350,413,343 | 31,889,779 out of 32,180,345 |