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Pythium irregulare vs Guillardia theta CCMP2712 LastZ results

Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium irregulare 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 irregulareGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,893 alignment blocks

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

Uncovered: 40,688,106 out of 42,968,084
Covered: 2,279,978 out of 42,968,084

Uncovered: 18,498,789 out of 20,543,058
Matches: 1,250,932 out of 20,543,058
Mismatches: 702,623 out of 20,543,058
Insertions: 90,714 out of 20,543,058
Identity over aligned base-pairs: 61.2%

Guillardia theta CCMP2712

Uncovered: 84,927,480 out of 87,266,873
Covered: 2,339,393 out of 87,266,873

Uncovered: 28,551,505 out of 30,644,092
Matches: 1,283,818 out of 30,644,092
Mismatches: 717,370 out of 30,644,092
Insertions: 91,399 out of 30,644,092
Identity over aligned base-pairs: 61.4%

Block size distribution

Size range All 8,893 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
35
155.0 bp
10 bp - 100 bp
2,222
152.4 kb
518
36.4 kb
100 bp - 1 kb
6,005
2.0 Mb
3,053
1.3 Mb
1 kb - 10 kb
631
1.1 Mb
918
1.7 Mb
10 kb - 100 kb
14
171.4 kb