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Phytophthora lateralis vs Phytophthora parasitica LastZ results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora lateralis 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 lateralisPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 64,339 alignment blocks

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

Uncovered: 10,782,839 out of 43,981,379
Covered: 33,198,540 out of 43,981,379

Uncovered: 551,807 out of 14,242,768
Matches: 10,438,968 out of 14,242,768
Mismatches: 2,999,679 out of 14,242,768
Insertions: 252,314 out of 14,242,768
Identity over aligned base-pairs: 76.2%

Phytophthora parasitica

Uncovered: 19,475,143 out of 55,229,644
Covered: 35,754,501 out of 55,229,644

Uncovered: 5,227,148 out of 27,601,672
Matches: 16,341,176 out of 27,601,672
Mismatches: 5,586,879 out of 27,601,672
Insertions: 446,469 out of 27,601,672
Identity over aligned base-pairs: 73.0%

Block size distribution

Size range All 64,339 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
554
3.0 kb
10 bp - 100 bp
8,779
573.3 kb
4,217
298.6 kb
100 bp - 1 kb
42,022
16.0 Mb
23,035
8.9 Mb
1 kb - 10 kb
12,836
28.6 Mb
9,786
23.8 Mb
10 kb - 100 kb
148
2.1 Mb
716
14.1 Mb
100 kb - 1 Mb
1
120.2 kb