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Pythium arrhenomanes vs Pythium iwayamai LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium arrhenomanes 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 arrhenomanesPythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 43,925 alignment blocks

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

Uncovered: 25,039,090 out of 44,672,625
Covered: 19,633,535 out of 44,672,625

Uncovered: 4,160,760 out of 18,367,184
Matches: 9,431,393 out of 18,367,184
Mismatches: 4,257,148 out of 18,367,184
Insertions: 517,883 out of 18,367,184
Identity over aligned base-pairs: 66.4%

Pythium iwayamai

Uncovered: 23,474,349 out of 43,199,174
Covered: 19,724,825 out of 43,199,174

Uncovered: 4,461,792 out of 19,552,457
Matches: 9,902,132 out of 19,552,457
Mismatches: 4,534,319 out of 19,552,457
Insertions: 654,214 out of 19,552,457
Identity over aligned base-pairs: 65.6%

Block size distribution

Size range All 43,925 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
144
784.0 bp
10 bp - 100 bp
4,781
328.3 kb
1,440
105.0 kb
100 bp - 1 kb
32,478
13.0 Mb
13,238
5.7 Mb
1 kb - 10 kb
6,510
11.0 Mb
6,983
16.8 Mb
10 kb - 100 kb
12
143.0 kb
136
1.8 Mb