In this section

Tetrahymena thermophila vs Phytophthora parasitica LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,300 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 101,813,924 out of 103,014,375
Covered: 1,200,451 out of 103,014,375

Uncovered: 47,076,555 out of 48,193,658
Matches: 654,833 out of 48,193,658
Mismatches: 431,151 out of 48,193,658
Insertions: 31,119 out of 48,193,658
Identity over aligned base-pairs: 58.6%

Phytophthora parasitica

Uncovered: 54,207,112 out of 55,229,644
Covered: 1,022,532 out of 55,229,644

Uncovered: 26,610,077 out of 27,601,672
Matches: 580,885 out of 27,601,672
Mismatches: 383,439 out of 27,601,672
Insertions: 27,271 out of 27,601,672
Identity over aligned base-pairs: 58.6%

Block size distribution

Size range All 5,300 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
26
115.0 bp
10 bp - 100 bp
1,014
72.0 kb
387
28.4 kb
100 bp - 1 kb
4,114
1.3 Mb
1,929
768.1 kb
1 kb - 10 kb
146
217.7 kb
379
723.6 kb
10 kb - 100 kb
4
44.7 kb