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Pythium arrhenomanes vs Guillardia theta CCMP2712 LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium arrhenomanes was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterPythium arrhenomanesGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,250 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium arrhenomanes

Uncovered: 42,542,192 out of 44,672,625
Covered: 2,130,433 out of 44,672,625

Uncovered: 16,563,739 out of 18,367,184
Matches: 1,100,087 out of 18,367,184
Mismatches: 626,370 out of 18,367,184
Insertions: 76,988 out of 18,367,184
Identity over aligned base-pairs: 61.0%

Guillardia theta CCMP2712

Uncovered: 85,000,315 out of 87,266,873
Covered: 2,266,558 out of 87,266,873

Uncovered: 28,626,039 out of 30,644,092
Matches: 1,223,909 out of 30,644,092
Mismatches: 708,418 out of 30,644,092
Insertions: 85,726 out of 30,644,092
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 8,250 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
32
171.0 bp
10 bp - 100 bp
1,885
131.8 kb
440
32.3 kb
100 bp - 1 kb
5,759
1.9 Mb
3,071
1.3 Mb
1 kb - 10 kb
573
940.3 kb
843
1.6 Mb
10 kb - 100 kb
1
10.1 kb
10
121.0 kb