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Phytophthora kernoviae vs Guillardia theta CCMP2712 LastZ results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora kernoviae 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 kernoviaeGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,989 alignment blocks

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

Uncovered: 41,086,539 out of 43,208,681
Covered: 2,122,142 out of 43,208,681

Uncovered: 9,845,585 out of 11,344,308
Matches: 919,257 out of 11,344,308
Mismatches: 524,322 out of 11,344,308
Insertions: 55,144 out of 11,344,308
Identity over aligned base-pairs: 61.3%

Guillardia theta CCMP2712

Uncovered: 85,124,690 out of 87,266,873
Covered: 2,142,183 out of 87,266,873

Uncovered: 28,715,965 out of 30,644,092
Matches: 1,171,217 out of 30,644,092
Mismatches: 675,127 out of 30,644,092
Insertions: 81,783 out of 30,644,092
Identity over aligned base-pairs: 60.7%

Block size distribution

Size range All 7,989 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
30
174.0 bp
10 bp - 100 bp
1,864
130.0 kb
399
28.7 kb
100 bp - 1 kb
5,517
1.9 Mb
2,678
1.1 Mb
1 kb - 10 kb
578
936.0 kb
899
1.6 Mb
10 kb - 100 kb
11
134.5 kb