Drosophila melanogaster vs Drosophila persimilis LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila persimilis (Drosophila persimilis, dper_caf1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 78. Drosophila melanogaster was used as the reference species. After running LastZ, the raw LastZ 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.

Results

Number of alignment blocks: 145,142

Genome coverage (bp) Coding exon coverage (bp)
Drosophila melanogaster

Uncovered: 64,479,707 out of 143,725,995
Covered: 79,246,288 out of 143,725,995

Uncovered: 1,842,630 out of 22,883,909
Matches: 15,844,787 out of 22,883,909
Mismatches: 4,758,046 out of 22,883,909
Insertions: 438,446 out of 22,883,909

Drosophila persimilis

Uncovered: 103,383,733 out of 188,374,079
Covered: 84,990,346 out of 188,374,079

Uncovered: 1,703,169 out of 21,669,015
Matches: 14,891,214 out of 21,669,015
Mismatches: 4,470,042 out of 21,669,015
Insertions: 604,590 out of 21,669,015

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Drosophila melanogaster Drosophila persimilis
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}