In this section

Phytophthora ramorum vs Guillardia theta CCMP2712 LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora ramorum 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

ParameterPhytophthora ramorumGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 9,014 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora ramorum

Uncovered: 64,053,460 out of 66,652,401
Covered: 2,598,941 out of 66,652,401

Uncovered: 20,053,383 out of 22,377,278
Matches: 1,417,178 out of 22,377,278
Mismatches: 807,736 out of 22,377,278
Insertions: 98,981 out of 22,377,278
Identity over aligned base-pairs: 61.0%

Guillardia theta CCMP2712

Uncovered: 84,827,353 out of 87,266,873
Covered: 2,439,520 out of 87,266,873

Uncovered: 28,550,448 out of 30,644,092
Matches: 1,234,242 out of 30,644,092
Mismatches: 768,911 out of 30,644,092
Insertions: 90,491 out of 30,644,092
Identity over aligned base-pairs: 59.0%

Block size distribution

Size range All 9,014 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
31
179.0 bp
10 bp - 100 bp
2,119
146.7 kb
482
34.7 kb
100 bp - 1 kb
6,127
2.1 Mb
3,066
1.3 Mb
1 kb - 10 kb
733
1.3 Mb
1,044
2.0 Mb
10 kb - 100 kb
4
55.5 kb
22
275.5 kb