Anopheles albimanus vs Anopheles culicifacies LastZ Results

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Anopheles albimanus (Anopheles albimanus, AalbS2) and Anopheles culicifacies (Anopheles culicifacies, AculA1) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Anopheles albimanus 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: 105,020

Genome coverage (bp) Coding exon coverage (bp)
Anopheles albimanus

Uncovered: 137,841,093 out of 173,339,240
Covered: 35,498,147 out of 173,339,240

Uncovered: 1,836,338 out of 20,837,397
Matches: 13,725,496 out of 20,837,397
Mismatches: 4,570,059 out of 20,837,397
Insertions: 705,504 out of 20,837,397

Anopheles culicifacies

Uncovered: 167,650,479 out of 202,998,806
Covered: 35,348,327 out of 202,998,806

Uncovered: 2,024,730 out of 20,898,504
Matches: 13,822,743 out of 20,898,504
Mismatches: 4,583,352 out of 20,898,504
Insertions: 467,679 out of 20,898,504

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

Anopheles albimanus Anopheles culicifacies
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}