In this section

Pythium vexans vs Guillardia theta CCMP2712 LastZ results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium vexans 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 vexansGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 9,066 alignment blocks

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

Uncovered: 31,436,949 out of 33,844,883
Covered: 2,407,934 out of 33,844,883

Uncovered: 16,477,078 out of 18,608,353
Matches: 1,298,933 out of 18,608,353
Mismatches: 733,003 out of 18,608,353
Insertions: 99,339 out of 18,608,353
Identity over aligned base-pairs: 60.9%

Guillardia theta CCMP2712

Uncovered: 84,832,823 out of 87,266,873
Covered: 2,434,050 out of 87,266,873

Uncovered: 28,487,052 out of 30,644,092
Matches: 1,325,596 out of 30,644,092
Mismatches: 734,433 out of 30,644,092
Insertions: 97,011 out of 30,644,092
Identity over aligned base-pairs: 61.5%

Block size distribution

Size range All 9,066 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
25
138.0 bp
10 bp - 100 bp
2,134
145.6 kb
514
35.0 kb
100 bp - 1 kb
6,235
2.1 Mb
3,158
1.3 Mb
1 kb - 10 kb
671
1.1 Mb
982
1.8 Mb
10 kb - 100 kb
1
10.6 kb
16
192.4 kb