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Human vs Human LastZ alignments

Human (Homo sapiens, GRCh37) and Human (Homo sapiens, GRCh37) alignments were downloaded from UCSC in Ensembl release 66.

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: 104,167

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

Uncovered: 2,871,198,124 out of 3,098,825,702
Covered: 227,627,578 out of 3,098,825,702

Uncovered: 30,254,523 out of 35,313,516
Matches: 4,697,666 out of 35,313,516
Mismatches: 305,942 out of 35,313,516
Insertions: 55,385 out of 35,313,516

Homo sapiens

Uncovered: 2,871,198,124 out of 3,098,825,702
Covered: 227,627,578 out of 3,098,825,702

Uncovered: 30,254,523 out of 35,313,516
Matches: 4,697,666 out of 35,313,516
Mismatches: 305,942 out of 35,313,516
Insertions: 55,385 out of 35,313,516