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Tetrahymena thermophila vs Pythium arrhenomanes LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,249 alignment blocks

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

Uncovered: 102,260,748 out of 103,014,375
Covered: 753,627 out of 103,014,375

Uncovered: 47,473,252 out of 48,193,658
Matches: 415,304 out of 48,193,658
Mismatches: 291,553 out of 48,193,658
Insertions: 13,549 out of 48,193,658
Identity over aligned base-pairs: 57.6%

Pythium arrhenomanes

Uncovered: 44,032,226 out of 44,672,625
Covered: 640,399 out of 44,672,625

Uncovered: 17,796,066 out of 18,367,184
Matches: 330,751 out of 18,367,184
Mismatches: 227,685 out of 18,367,184
Insertions: 12,682 out of 18,367,184
Identity over aligned base-pairs: 57.9%

Block size distribution

Size range All 3,249 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
55.0 bp
10 bp - 100 bp
553
40.1 kb
158
11.9 kb
100 bp - 1 kb
2,607
771.9 kb
1,261
468.1 kb
1 kb - 10 kb
78
112.1 kb
219
432.5 kb
10 kb - 100 kb
1
11.7 kb