In this section

Pythium iwayamai vs Guillardia theta CCMP2712 LastZ results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium iwayamai 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 iwayamaiGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,986 alignment blocks

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

Uncovered: 41,008,248 out of 43,199,174
Covered: 2,190,926 out of 43,199,174

Uncovered: 17,668,322 out of 19,552,457
Matches: 1,156,646 out of 19,552,457
Mismatches: 643,457 out of 19,552,457
Insertions: 84,032 out of 19,552,457
Identity over aligned base-pairs: 61.4%

Guillardia theta CCMP2712

Uncovered: 84,989,052 out of 87,266,873
Covered: 2,277,821 out of 87,266,873

Uncovered: 28,613,711 out of 30,644,092
Matches: 1,237,847 out of 30,644,092
Mismatches: 708,051 out of 30,644,092
Insertions: 84,483 out of 30,644,092
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 8,986 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
34
192.0 bp
10 bp - 100 bp
2,169
148.9 kb
477
34.2 kb
100 bp - 1 kb
6,271
2.1 Mb
3,250
1.3 Mb
1 kb - 10 kb
512
867.7 kb
838
1.6 Mb
10 kb - 100 kb
12
145.7 kb