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Tetrahymena thermophila vs Pythium vexans LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_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 thermophilaPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,263 alignment blocks

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

Uncovered: 102,251,608 out of 103,014,375
Covered: 762,767 out of 103,014,375

Uncovered: 47,469,044 out of 48,193,658
Matches: 418,234 out of 48,193,658
Mismatches: 292,931 out of 48,193,658
Insertions: 13,449 out of 48,193,658
Identity over aligned base-pairs: 57.7%

Pythium vexans

Uncovered: 33,196,123 out of 33,844,883
Covered: 648,760 out of 33,844,883

Uncovered: 18,008,246 out of 18,608,353
Matches: 345,163 out of 18,608,353
Mismatches: 242,454 out of 18,608,353
Insertions: 12,490 out of 18,608,353
Identity over aligned base-pairs: 57.5%

Block size distribution

Size range All 3,263 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
32.0 bp
10 bp - 100 bp
547
41.1 kb
198
15.8 kb
100 bp - 1 kb
2,633
792.8 kb
1,240
476.7 kb
1 kb - 10 kb
74
106.7 kb
211
425.8 kb
10 kb - 100 kb
2
22.4 kb