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Phytophthora lateralis vs Guillardia theta CCMP2712 LastZ results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 lateralisGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,958 alignment blocks

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

Uncovered: 42,185,939 out of 43,981,379
Covered: 1,795,440 out of 43,981,379

Uncovered: 12,710,303 out of 14,242,768
Matches: 928,096 out of 14,242,768
Mismatches: 538,150 out of 14,242,768
Insertions: 66,219 out of 14,242,768
Identity over aligned base-pairs: 60.6%

Guillardia theta CCMP2712

Uncovered: 85,320,625 out of 87,266,873
Covered: 1,946,248 out of 87,266,873

Uncovered: 28,909,571 out of 30,644,092
Matches: 1,052,973 out of 30,644,092
Mismatches: 604,743 out of 30,644,092
Insertions: 76,805 out of 30,644,092
Identity over aligned base-pairs: 60.7%

Block size distribution

Size range All 6,958 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
26
121.0 bp
10 bp - 100 bp
1,574
108.1 kb
363
25.7 kb
100 bp - 1 kb
4,840
1.7 Mb
2,463
1.0 Mb
1 kb - 10 kb
518
853.8 kb
758
1.4 Mb
10 kb - 100 kb
14
169.8 kb