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Human vs Alpaca BlastZ alignments

Human (Homo sapiens, GRCh37) and Alpaca (Vicugna pacos, vicPac1) 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.

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Results

Number of alignment blocks: 1,651,937

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 1,914,341,619 out of 3,098,825,702
Covered: 1,184,484,083 out of 3,098,825,702

Uncovered: 9,680,955 out of 35,313,516
Matches: 21,620,662 out of 35,313,516
Mismatches: 3,766,720 out of 35,313,516
Insertions: 245,179 out of 35,313,516

Vicugna pacos

Uncovered: 1,870,168,018 out of 2,967,729,481
Covered: 1,097,561,463 out of 2,967,729,481

Uncovered: 2,812,633 out of 18,994,395
Matches: 14,437,355 out of 18,994,395
Mismatches: 1,713,932 out of 18,994,395
Insertions: 30,475 out of 18,994,395