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Phytophthora ramorum vs Tetrahymena thermophila LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 ramorumTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,865 alignment blocks

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

Uncovered: 65,712,118 out of 66,652,401
Covered: 940,283 out of 66,652,401

Uncovered: 21,519,068 out of 22,377,278
Matches: 500,433 out of 22,377,278
Mismatches: 337,449 out of 22,377,278
Insertions: 20,328 out of 22,377,278
Identity over aligned base-pairs: 58.3%

Tetrahymena thermophila

Uncovered: 101,936,632 out of 103,014,375
Covered: 1,077,743 out of 103,014,375

Uncovered: 47,219,404 out of 48,193,658
Matches: 558,300 out of 48,193,658
Mismatches: 393,753 out of 48,193,658
Insertions: 22,201 out of 48,193,658
Identity over aligned base-pairs: 57.3%

Block size distribution

Size range All 4,865 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
87.0 bp
10 bp - 100 bp
1,084
81.4 kb
468
36.8 kb
100 bp - 1 kb
3,619
1.1 Mb
1,761
655.8 kb
1 kb - 10 kb
147
233.7 kb
337
682.5 kb
10 kb - 100 kb
2
22.6 kb