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Phytophthora infestans vs Tetrahymena thermophila LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora infestans 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 infestansTetrahymena thermophila
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 9,292 alignment blocks

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

Uncovered: 227,043,454 out of 228,543,505
Covered: 1,500,051 out of 228,543,505

Uncovered: 21,451,497 out of 22,421,425
Matches: 569,331 out of 22,421,425
Mismatches: 375,045 out of 22,421,425
Insertions: 25,552 out of 22,421,425
Identity over aligned base-pairs: 58.7%

Tetrahymena thermophila

Uncovered: 101,407,121 out of 103,014,375
Covered: 1,607,254 out of 103,014,375

Uncovered: 46,936,437 out of 48,193,658
Matches: 630,300 out of 48,193,658
Mismatches: 598,524 out of 48,193,658
Insertions: 28,397 out of 48,193,658
Identity over aligned base-pairs: 50.1%

Block size distribution

Size range All 9,292 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
195
850.0 bp
10 bp - 100 bp
3,780
293.0 kb
1,112
90.6 kb
100 bp - 1 kb
5,100
1.5 Mb
3,228
1.1 Mb
1 kb - 10 kb
203
396.8 kb
433
893.4 kb
10 kb - 100 kb
14
218.1 kb
17
253.8 kb