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Pythium ultimum vs Guillardia theta CCMP2712 LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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 ultimumGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,753 alignment blocks

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

Uncovered: 42,519,150 out of 44,913,582
Covered: 2,394,432 out of 44,913,582

Uncovered: 17,757,066 out of 19,826,256
Matches: 1,255,578 out of 19,826,256
Mismatches: 726,511 out of 19,826,256
Insertions: 87,101 out of 19,826,256
Identity over aligned base-pairs: 60.7%

Guillardia theta CCMP2712

Uncovered: 84,964,491 out of 87,266,873
Covered: 2,302,382 out of 87,266,873

Uncovered: 28,614,613 out of 30,644,092
Matches: 1,230,263 out of 30,644,092
Mismatches: 714,584 out of 30,644,092
Insertions: 84,632 out of 30,644,092
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 8,753 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
28
125.0 bp
10 bp - 100 bp
2,130
146.9 kb
493
34.6 kb
100 bp - 1 kb
5,954
2.0 Mb
2,922
1.2 Mb
1 kb - 10 kb
639
1.1 Mb
944
1.8 Mb
10 kb - 100 kb
2
47.1 kb
17
247.3 kb