In this section

Tetrahymena thermophila vs Pythium aphanidermatum LastZ results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,023 alignment blocks

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

Uncovered: 101,824,290 out of 103,014,375
Covered: 1,190,085 out of 103,014,375

Uncovered: 47,081,458 out of 48,193,658
Matches: 646,369 out of 48,193,658
Mismatches: 436,169 out of 48,193,658
Insertions: 29,662 out of 48,193,658
Identity over aligned base-pairs: 58.1%

Pythium aphanidermatum

Uncovered: 34,892,556 out of 35,876,849
Covered: 984,293 out of 35,876,849

Uncovered: 17,143,356 out of 18,015,574
Matches: 511,079 out of 18,015,574
Mismatches: 337,450 out of 18,015,574
Insertions: 23,689 out of 18,015,574
Identity over aligned base-pairs: 58.6%

Block size distribution

Size range All 5,023 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
29
127.0 bp
10 bp - 100 bp
957
70.7 kb
387
30.4 kb
100 bp - 1 kb
3,898
1.2 Mb
1,832
740.4 kb
1 kb - 10 kb
139
219.6 kb
334
660.4 kb
10 kb - 100 kb
5
57.3 kb